Application of micro-solid-phase extraction for the on-site extraction of heterocyclic aromatic amines in seawater.

PubMed

Basheer, Chanbasha

2018-04-01

An efficient on-site extraction technique to determine carcinogenic heterocyclic aromatic amines in seawater has been reported. A micro-solid-phase extraction device placed inside a portable battery-operated pump was used for the on-site extraction of seawater samples. Before on-site applications, parameters that influence the extraction efficiency (extraction time, type of sorbent materials, suitable desorption solvent, desorption time, and sample volume) were investigated and optimized in the laboratory. The developed method was then used for the on-site sampling of heterocyclic aromatic amines determination in seawater samples close to distillation plant. Once the on-site extraction completed, the small extraction device with the analytes was brought back to the laboratory for analysis using high-performance liquid chromatography with fluorescence detection. Based on the optimized conditions, the calibration curves were linear over the concentration range of 0.05-20 μg/L with correlation coefficients up to 0.996. The limits of detection were 0.004-0.026 μg/L, and the reproducibility values were between 1.3 and 7.5%. To evaluate the extraction efficiency, a comparison was made with conventional solid-phase extraction and it was applied to various fortified real seawater samples. The average relative recoveries obtained from the spiked seawater samples varied in the range 79.9-95.2%. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Polybenzimidazole via aromatic nucleophilic displacement

NASA Technical Reports Server (NTRS)

Connell, John W. (Inventor); Hergenrother, Paul M. (Inventor); Smith, Joseph G. (Inventor)

1994-01-01

Di(hydroxyphenyl)benzimidazole monomers were prepared from phenyl-4-hydroxybenzoate and aromatic bis(o-diamine)s. These monomers were used in the synthesis of soluble polybenzimidazoles. The reaction involved the aromatic nucleophilic displacement of various di(hydroxyphenyl)benzimidazole monomers with activated aromatic dihalides or activated aromatic dinitro compounds in the presence of an alkali metal base. These polymers exhibited lower glass transition temperatures, improved solubility, and better compression moldability over their commercial counterparts.

Polyimidazoles via aromatic nucleophilic displacement

NASA Technical Reports Server (NTRS)

Connell, John W. (Inventor); Hergenrother, Paul M. (Inventor)

1992-01-01

Polyimidazoles (PI) are prepared by the aromatic nucleophilic displacement reaction of di(hydroxyphenyl) imidazole monomers with activated aromatic dihalides or activated aromatic dinitro compounds. The reactions are carried out in polar aprotic solvents such as N,N-dimethyl acetamide, sulfolane, N-methylpyrrolidinone, dimethylsulfoxide, or diphenylsulfone using alkali metal bases such as potassium carbonate at elevated temperatures under nitrogen. The di(hydroxyphenyl) imidazole monomers are prepared by reacting an aromatic aldehyde with a dimethoxybenzil or by reacting an aromatic dialdehyde with a methoxybenzil in the presence of ammonium acetate. The di(methoxyphenyl) imidazole is subsequently treated with aqueous hydrobromic acid to give the di(hydroxphenyl) imidazole monomer. This synthetic route has provided high molecular weight PI of new chemical structure, is economically and synthetically more favorable than other routes, and allows for facile chemical structure variation due to the availability of a large variety of activated aromatic dihalides and dinitro compounds.

Polyimidazoles via aromatic nucleophilic displacement

NASA Technical Reports Server (NTRS)

Hergenrother, Paul M. (Inventor); Connell, John W. (Inventor)

1991-01-01

Polyimidazoles (Pl) are prepared by the aromatic nucleophilic displacement reaction of di(hydroxyphenyl)imidazole monomers with activated aromatic dihalides or activated aromatic dinitro compounds. The reactions are carried out in polar aprotic solvents such as N,N-dimethylacetamide, sulfolane, N-methylpyrroldinone, dimethylsulfoxide, or diphenylsulfone using alkali metal bases such as potassium carbonate at elevated temperature under nitrogen. The di(hydroxyphenyl)imidazole monomers are prepared by reacting an aromatic aldehyde with a dimethoxybenzil or by reacting an aromatic dialdehyde with a methoxybenzil in the presence of ammonium acetate. The di(methoxyphenyl)imidazole is subsequently treated with aqueous hydrobromic acid to give the di(hydroxyphenyl)imidazole monomer. This synthetic route has provided high molecular weight Pl of new chemical structure, is economically and synthetically more favorable than other routes, and allows for facile chemical structure variation due to the availability of a large variety of activated aromatic dihalides and dinitro compounds.

Synthesis of tetra- and octa-aurated heteroaryl complexes towards probing aromatic indoliums

PubMed Central

Yuan, Jun; Sun, Tingting; He, Xin; An, Ke; Zhu, Jun; Zhao, Liang

2016-01-01

Polymetalated aromatic compounds are particularly challenging synthetic goals because of the limited thermodynamic stability of polyanionic species arising from strong electrostatic repulsion between adjacent carbanionic sites. Here we describe a facile synthesis of two polyaurated complexes including a tetra-aurated indole and an octa-aurated benzodipyrrole. The imido trinuclear gold(I) moiety exhibits nucleophilicity and undergoes an intramolecular attack on a gold(I)-activated ethynyl to generate polyanionic heteroaryl species. Their computed magnetic properties reveal the aromatic character in the five-membered ring. The incorporation of the aurated substituents at the nitrogen atom can convert non-aromaticity in the parent indolium into aromaticity in the aurated one because of hyperconjugation. Thus, the concept of hyperconjugative aromaticity is extended to heterocycles with transition metal substituents. More importantly, further analysis indicates that the aurated substituents can perform better than traditional main-group substituents. This work highlights the difference in aromaticity between polymetalated aryls and their organic prototypes. PMID:27186982

Evaluating the Substrate Selectivity of Alkyladenine DNA Glycosylase: The Synergistic Interplay of Active Site Flexibility and Water Reorganization.

PubMed

Lenz, Stefan A P; Wetmore, Stacey D

2016-02-09

Human alkyladenine DNA glycosylase (AAG) functions as part of the base excision repair (BER) pathway by cleaving the N-glycosidic bond that connects nucleobases to the sugar-phosphate backbone in DNA. AAG targets a range of structurally diverse purine lesions using nonspecific DNA-protein π-π interactions. Nevertheless, the enzyme discriminates against the natural purines and is inhibited by pyrimidine lesions. This study uses molecular dynamics simulations and seven different neutral or charged substrates, inhibitors, or canonical purines to probe how the bound nucleotide affects the conformation of the AAG active site, and the role of active site residues in dictating substrate selectivity. The neutral substrates form a common DNA-protein hydrogen bond, which results in a consistent active site conformation that maximizes π-π interactions between the aromatic residues and the nucleobase required for catalysis. Nevertheless, subtle differences in DNA-enzyme contacts for different neutral substrates explain observed differential catalytic efficiencies. In contrast, the exocyclic amino groups of the natural purines clash with active site residues, which leads to catalytically incompetent DNA-enzyme complexes due to significant reorganization of active site water. Specifically, water resides between the A nucleobase and the active site aromatic amino acids required for catalysis, while a shift in the position of the general base (E125) repositions (potentially nucleophilic) water away from G. Despite sharing common amino groups, the methyl substituents in cationic purine lesions (3MeA and 7MeG) exhibit repulsion with active site residues, which repositions the damaged bases in the active site in a manner that promotes their excision. Overall, we provide a structural explanation for the diverse yet discriminatory substrate selectivity of AAG and rationalize key kinetic data available for the enzyme. Specifically, our results highlight the complex interplay of many

Anti-aging activities of extracts from Tunisian medicinal halophytes and their aromatic constituents

PubMed Central

Jdey, A.; Falleh, H.; Ben Jannet, S.; Mkadmini Hammi, K.; Dauvergne, X.; Magné, C.; Ksouri, R.

2017-01-01

Six medicinal halophytes widely represented in North Africa and commonly used in traditional medicine were screened for pharmacological properties to set out new promising sources of natural ingredients for cosmetic or nutraceutical applications. Thus, Citrullus colocynthis, Cleome arabica, Daemia cordata, Haloxylon articulatum, Pituranthos scoparius and Scorzonera undulata were examined for their in vitro antioxidant (DPPH scavenging and superoxide anion-scavenging, β-carotene bleaching inhibition and iron-reducing tests), antibacterial (microdilution method, against four human pathogenic bacteria) and anti-tyrosinase activities. Besides, their aromatic composition was determined by RP-HPLC. H. articulatum shoot extracts exhibited the strongest antioxidant activity and inhibited efficiently the growth of Salmonella enterica and Escherichia coli. P. scoparius and C. arabica inhibited slightly monophenolase, whereas H. articulatum was the most efficient inhibitor of diphenolase activity. Furthermore, H. articulatum exhibited the highest aromatic content (3.4 % DW), with dopamine as the major compound. These observations suggest that shoot extract of H. articulatum, and to a lesser extent of C. arabica, could be used as antioxidant, antibiotic as well as new natural skin lightening agents. Also, possible implication of aromatic compounds in anti-tyrosinase activity is discussed. PMID:28827992

Anti-aging activities of extracts from Tunisian medicinal halophytes and their aromatic constituents.

PubMed

Jdey, A; Falleh, H; Ben Jannet, S; Mkadmini Hammi, K; Dauvergne, X; Magné, C; Ksouri, R

2017-01-01

Six medicinal halophytes widely represented in North Africa and commonly used in traditional medicine were screened for pharmacological properties to set out new promising sources of natural ingredients for cosmetic or nutraceutical applications. Thus, Citrullus colocynthis , Cleome arabica , Daemia cordata , Haloxylon articulatum , Pituranthos scoparius and Scorzonera undulata were examined for their in vitro antioxidant (DPPH scavenging and superoxide anion-scavenging, β -carotene bleaching inhibition and iron-reducing tests), antibacterial (microdilution method, against four human pathogenic bacteria) and anti-tyrosinase activities. Besides, their aromatic composition was determined by RP-HPLC. H. articulatum shoot extracts exhibited the strongest antioxidant activity and inhibited efficiently the growth of Salmonella enterica and Escherichia coli . P. scoparius and C. arabica inhibited slightly monophenolase, whereas H. articulatum was the most efficient inhibitor of diphenolase activity. Furthermore, H. articulatum exhibited the highest aromatic content (3.4 % DW), with dopamine as the major compound. These observations suggest that shoot extract of H. articulatum , and to a lesser extent of C. arabica , could be used as antioxidant, antibiotic as well as new natural skin lightening agents. Also, possible implication of aromatic compounds in anti-tyrosinase activity is discussed.

Active site and laminarin binding in glycoside hydrolase family 55

DOE PAGES

Bianchetti, Christopher M.; Takasuka, Taichi E.; Deutsch, Sam; ...

2015-03-09

The Carbohydrate Active Enzyme (CAZy) database indicates that glycoside hydrolase family 55 (GH55) contains both endo- and exo-β-1,3-glucanases. The founding structure in the GH55 is PcLam55A from the white rot fungus Phanerochaete chrysosporium. Here, we present high resolution crystal structures of bacterial SacteLam55A from the highly cellulolytic Streptomyces sp. SirexAA-E with bound substrates and product. These structures, along with mutagenesis and kinetic studies, implicate Glu-502 as the catalytic acid (as proposed earlier for Glu-663 in PcLam55A) and a proton relay network of four residues in activating water as the nucleophile. Further, a set of conserved aromatic residues that define themore » active site apparently enforce an exo-glucanase reactivity as demonstrated by exhaustive hydrolysis reactions with purified laminarioligosaccharides. Two additional aromatic residues that line the substrate-binding channel show substrate-dependent conformational flexibility that may promote processive reactivity of the bound oligosaccharide in the bacterial enzymes. Gene synthesis carried out on ~30% of the GH55 family gave 34 active enzymes (19% functional coverage of the nonredundant members of GH55). These active enzymes reacted with only laminarin from a panel of 10 different soluble and insoluble polysaccharides and displayed a broad range of specific activities and optima for pH and temperature. Furthermore, application of this experimental method provides a new, systematic way to annotate glycoside hydrolase phylogenetic space for functional properties.« less

Toxicity of N-substituted aromatics to acetoclastic methanogenic activity in granular sludge

DOE Office of Scientific and Technical Information (OSTI.GOV)

Donlon, B.A.; Razo-Flores, E.; Field, J.A.

1995-11-01

N-substituted aromatics are important priority pollutants entering the environment primarily through anthropogenic activities associated associated with the industrial production of dyes, explosives, pestides, and pharmaceuticals. Anaerobic treatment of wastewaters discharged by these industries could potentially be problematical as a result of the high toxicity of N-substituted aromatics. The objective of this study was to examine the structure-toxicity relationship of N-substituted aromatic compounds to acetoclastic methanogenic bacteria. The toxicity was assayed to serum flasks by measuring methane production in granular sludge. Unacclimated cultures were used to minimize the biotransformation of the toxic organic chemicals during the test. The nature and themore » degree of the aromatic substitution were observed to have a profound effect on the toxicity of the test compound. Nitroaromatic compounds were, on the average, over 500-fold more toxic than their corresponding aromatic amines. Considering the facile reduction of nitro groups by anerobic microorganisms, a dramatic detoxification of nitroaromatics towards methanogens can be expected to occur during anaerobic wastewater treatment. While the toxicity exerted by the N-substituted aromatic compounds was closely correlated with compound apolarity (log P), it was observed that at any given log P, N-substituted phenols had a toxicity that was 2 orders of magnitude higher than that of chlorophenols and alkylphenols. This indicates that toxicity due to the chemical reactivity of nitroaromatics is much more important than partitioning effects in bacterial membranes. 41 refs., 3 figs., 1 tab.« less

Catalytic co-aromatization of ethanol and methane

DOE PAGES

Wang, Aiguo; He, Peng; Yung, Matthew; ...

2016-06-06

This study demonstrates the technical feasibility of simultaneously converting ethanol and methane into liquid hydrocarbons at mild reaction conditions (400 °C and 1 atm) over silver and/or zinc modified zeolite catalysts. After GC-MS analysis, it is worth noting that aromatics are the major compounds contained in the liquid product collected from the run when 1%Ag/ZSM-5, particularly after H 2 pretreatment, is charged. Compared to the performance exhibited from the run with pure HZSM-5 support engaged, Ag addition into the HZSM-5 framework favors aromatics formation, which might be closely associated with better Ag dispersion and more abundance of strong surface acidicmore » sites where aromatization might take place while Zn loading exerts a detrimental effect on the production of aromatics but promotes the ether generation possibly through dehydration reaction. Referred to that from its N 2 counterpart, the increased aromatics formation of the collected liquid product when methane is present indicates that methane existence might facilitate ethanol aromatization. Moreover, combined with the increased carbon number in the formed aromatics from CH 4 run when H 2 run is referred and zero liquid formation from CH 4-alone test as well as more prominent endothermic feature of methane run and more importantly the notably increased 13C signals in 13C NMR spectra of the liquid product collected during ethanol conversion under 13CH 4 environment, all the observations suggest that methane might be activated nonoxidatively and converted into higher hydrocarbons, preferentially into aromatics if suitable catalyst is charged under the assistance of co-existing oxygenated hydrocarbon. Lastly, the reported synergetic effect could potentially lead to the more economic utilization of abundant natural gas and cellulosic ethanol.« less

An Aromatic Cap Seals the Substrate Binding Site in an ECF-Type S Subunit for Riboflavin

DOE Office of Scientific and Technical Information (OSTI.GOV)

Karpowich, Nathan K.; Song, Jinmei; Wang, Da-Neng

2016-06-13

ECF transporters are a family of active membrane transporters for essential micronutrients, such as vitamins and trace metals. Found exclusively in archaea and bacteria, these transporters are composed of four subunits: an integral membrane substrate-binding subunit (EcfS), a transmembrane coupling subunit (EcfT), and two ATP-binding cassette ATPases (EcfA and EcfA'). We have characterized the structural basis of substrate binding by the EcfS subunit for riboflavin from Thermotoga maritima, TmRibU. TmRibU binds riboflavin with high affinity, and the protein–substrate complex is exceptionally stable in solution. The crystal structure of riboflavin-bound TmRibU reveals an electronegative binding pocket at the extracellular surface inmore » which the substrate is completely buried. Analysis of the intermolecular contacts indicates that nearly every available substrate hydrogen bond is satisfied. A conserved aromatic residue at the extracellular end of TM5, Tyr130, caps the binding site to generate a substrate-bound, occluded state, and non-conservative mutation of Tyr130 reduces the stability of this conformation. Using a novel fluorescence binding assay, we find that an aromatic residue at this position is essential for high-affinity substrate binding. Comparison with other S subunit structures suggests that TM5 and Loop5-6 contain a dynamic, conserved motif that plays a key role in gating substrate entry and release by S subunits of ECF transporters.« less

Metabolism and Biomarkers of Heterocyclic Aromatic Amines in Molecular Epidemiology Studies: Lessons Learned from Aromatic Amines

PubMed Central

2011-01-01

Aromatic amines and heterocyclic aromatic amines (HAAs) are structurally related classes of carcinogens that are formed during the combustion of tobacco or during the high-temperature cooking of meats. Both classes of procarcinogens undergo metabolic activation by N-hydroxylation of the exocyclic amine group, to produce a common proposed intermediate, the arylnitrenium ion, which is the critical metabolite implicated in toxicity and DNA damage. However, the biochemistry and chemical properties of these compounds are distinct and different biomarkers of aromatic amines and HAAs have been developed for human biomonitoring studies. Hemoglobin adducts have been extensively used as biomarkers to monitor occupational and environmental exposures to a number of aromatic amines; however, HAAs do not form hemoglobin adducts at appreciable levels and other biomarkers have been sought. A number of epidemiologic studies that have investigated dietary consumption of well-done meat in relation to various tumor sites reported a positive association between cancer risk and well-done meat consumption, although some studies have shown no associations between well-done meat and cancer risk. A major limiting factor in most epidemiological studies is the uncertainty in quantitative estimates of chronic exposure to HAAs and, thus, the association of HAAs formed in cooked meat and cancer risk has been difficult to establish. There is a critical need to establish long-term biomarkers of HAAs that can be implemented in molecular epidemioIogy studies. In this review article, we highlight and contrast the biochemistry of several prototypical carcinogenic aromatic amines and HAAs to which humans are chronically exposed. The biochemical properties and the impact of polymorphisms of the major xenobiotic-metabolizing enzymes on the biological effects of these chemicals are examined. Lastly, the analytical approaches that have been successfully employed to biomonitor aromatic amines and HAAs, and

Screening of some Greek aromatic plants for antioxidant activity.

PubMed

Couladis, Maria; Tzakou, Olga; Verykokidou, Evmorfia; Harvala, Catherine

2003-02-01

The role of antioxidants in preventing oxygen radical and hydrogen peroxide induced cytotoxicity and tissue damage in various human diseases is increasingly recognized. In this study the in vitro antioxidant activity of the ethanol extracts obtained from 21 aromatic plants belonging to the Lamiaceae family was investigated. Of the extracts tested, those of Salvia ringens, Salvia pomifera, Stachys spruneri, Origanum dictamnus, Phlomis lanata, Ballota pseudodictamnus, Ballota acetabulosa, Teucrium polium, Calamintha glandulosa and Micromeria graeca exhibited the same activity as alpha-tocopherol. Copyright 2003 John Wiley & Sons, Ltd.

Polybenzimidazoles Via Aromatic Nucleophilic Displacement

NASA Technical Reports Server (NTRS)

Connell, John W. (Inventor); Hergerrother, Paul M. (Inventor); Smith, Joseph G., Jr. (Inventor)

1997-01-01

Novel molecular weight controlled and endcapped polybenzimidazoles (PBI) are prepared by the aromatic nucleophilic displacement reaction of di(hydroxyphenylbenzimidazole) monomers with activated aromatic dihalides or activated aromatic dinitro compounds. The PBI are endcapped with mono(hydroxyphenyl)benzimidazoles. The polymerizations are carried out in polar aprotic solvents such as N-methyl-2-pyrrolidinone or N,N-dimethylacetamide using alkali metal bases such as potassium carbonate at elevated temperatures under nitrogen. Mono(hydroxyphenyl)benzimidazoles are synthesized by reacting phenyl-4-hydroxybenzoate with aromatic (o-diamine)s in diphenylsulfone. Molecular weight controlled and endcapped PBI of new chemical structures are prepared that exhibit a favorable combination of physical and mechanical properties.

Polybenzimidazoles via aromatic nucleophilic displacement

NASA Technical Reports Server (NTRS)

Connell, John W. (Inventor); Hergenrother, Paul M. (Inventor); Smith, Joseph G., Jr. (Inventor)

1995-01-01

Novel molecular weight controlled and endcapped polybenzimidazoles (PBI) are prepared by the aromatic nucleophilic displacement reaction of di(hydroxyphenyl benzimidazole) monomers with activated aromatic dihalides or activated aromatic dinitro compounds. The PBI are endcapped with mono(hydroxyphenyl) benzimidazoles. The polymerizations are carried out in polar aprotic solvents such as N-methyl-2-pyrrolidinone or N,N-dimethylacetamide using alkali metal bases such as potassium carbonate at elevated temperatures under nitrogen. Mono(hydroxyphenyl) benzimidazoles are synthesizedby reacting phenyl-4-hydroxybenzoate with aromatic (o-diamine)s in diphenylsulfone. Molecular weight controlled and endcapped PBI of new chemical structures are prepared that exhibit a favorable combination of physical and mechanical properties.

Differential levels of metabolites and enzymes related to aroma formation in aromatic indica rice varieties: comparison with non-aromatic varieties.

PubMed

Ghosh, Puja; Roychoudhury, Aryadeep

2018-01-01

Accounting for aroma production in different aromatic indica rice varieties based on variations in the levels of concerned metabolites and enzymes is poorly explored. The present investigation was, therefore, focused on unraveling the differential levels of metabolites and activities of enzymes related to aroma formation in eleven indigenous aromatic rice varieties, as compared with four non-aromatic varieties. The levels of metabolites such as proline (Pro) and Δ 1 -pyrroline-5-carboxylate (P5C), and the activity of related enzymes such as proline dehydrogenase (PDH), Δ 1 -pyrroline-5-carboxylate synthetase (P5CS), and ornithine aminotransferase (OAT) were comparatively higher in the aromatic varieties, with Kalonunia and Tulaipanji registering the highest Pro, Kalonunia the highest P5C content, Gobindobhog with the highest PDH activity, Gobindobhog and Tulaipanji with the highest P5CS, and Pusa Basmati-1 with the highest OAT activity. The levels of putrescine (Put) and γ-aminobutyric acid (GABA) were comparatively lower in aromatic varieties, with concomitant higher diamine oxidase (DAO) activity, especially in the varieties Gobindobhog and Tulaipanji. The betaine-aldehyde dehydrogenase 2 (BADH2) enzyme activity was remarkably lesser in aromatic varieties, especially Radhunipagal and Gobindobhog. Though the metabolites such as glycine-betaine and higher polyamines such as spermidine and spermine showed no specific trend with respect to their quantitative level in either aromatic or non-aromatic varieties, they were notably lower in the aromatic varieties such as Gobindobhog, Kalonunia, and Tulaipanji, indicating a possibility of their involvement in aroma formation. Therefore, the levels of metabolites such as Pro, P5C and methylglyoxal (MG), and the activity of enzymes such as PDH, P5CS, OAT, and DAO were comparatively higher in the aromatic rice varieties than the non-aromatic ones, whereas the levels of Put, GABA, and BADH2 were lower. Overall, the present

Synthesis and antibacterial activity of aromatic and heteroaromatic amino alcohols.

PubMed

de Almeida, Camila G; Reis, Samira G; de Almeida, Angelina M; Diniz, Claudio G; da Silva, Vânia L; Le Hyaric, Mireille

2011-11-01

Two series of aromatic and heteroaromatic amino alcohols were synthesized from alcohols and aldehydes and evaluated for their antibacterial activities. All the octylated compounds displayed a better activity against the four bacteria tested when evaluated by the agar diffusion method and were selected for the evaluation of minimal inhibitory concentration. The best results were obtained for p-octyloxybenzyl derivatives against Staphylococcus epidermidis (minimal inhibitory concentrations = 32 μm). © 2011 John Wiley & Sons A/S.

Noncomparative scaling of aromaticity through electron itinerancy

NASA Astrophysics Data System (ADS)

Paul, Satadal; Goswami, Tamal; Misra, Anirban

2015-10-01

Aromaticity is a multidimensional concept and not a directly observable. These facts have always stood in the way of developing an appropriate theoretical framework for scaling of aromaticity. In the present work, a quantitative account of aromaticity is developed on the basis of cyclic delocalization of π-electrons, which is the phenomenon leading to unique features of aromatic molecules. The stabilization in molecular energy, caused by delocalization of π-electrons is obtained as a second order perturbation energy for archetypal aromatic systems. The final expression parameterizes the aromatic stabilization energy in terms of atom to atom charge transfer integral, onsite repulsion energy and the population of spin orbitals at each site in the delocalized π-electrons. An appropriate computational platform is framed to compute each and individual parameter in the derived equation. The numerical values of aromatic stabilization energies obtained for various aromatic molecules are found to be in close agreement with available theoretical and experimental reports. Thus the reliable estimate of aromaticity through the proposed formalism renders it as a useful tool for the direct assessment of aromaticity, which has been a long standing problem in chemistry.

Activation of intestinal brush border guanylate cyclase by aromatic disulphide compounds.

PubMed Central

elDeib, M M; Parker, C D; White, A A

1991-01-01

Guanylate cyclase in pig intestinal brush border membranes was stimulated by certain aromatic disulphides. The most effective were 6-thioguanine disulphide [(TGS)2], 6-mercaptopurine disulphide, 6,6'-dithiodinicotinic acid, 5,5'-dithiobis-(2-nitrobenzoic acid) and 5-carboxy-2-thiouracil disulphide. (TGS)2 stimulated activity 15-fold when present at 0.1 mM. The optimum concentration for each disulphide was different, and higher concentrations were inhibitory. There was no activation by alkyl disulphides or by N-ethylmaleimide. Activation by 50 microM-(TGS)2 was partially reversed by later addition of 0.1 mM-dithiothreitol, whereas activation by the Escherichia coli heat-stable enterotoxin STa was relatively unaffected. Pretreatment of the membranes with (TGS)2 produced a concentration-dependent inhibition of STa-stimulated activity, while stimulating basal activity, until the activities were equal at 50 microM. Activity was [Mg2+]-dependent, the optimal [Mg2+] progressively increasing as the enzyme was stimulated by (TGS)2, STa and Lubrol PX respectively. However, (TGS)2 pretreatment prevented the shift to higher [Mg2+]optima induced by STa or Lubrol alone. Substitution of Mn2+ for Mg2+ in the reaction elevated basal activity and eliminated by activation (TGS)2. (TGS)2 only inhibited Mn2(+)-dependent activity (both basal and stimulated). The affinity of 125I-STa for its receptor was slightly increased by (TGS)2. We propose that (TGS)2 undergoes thiol-disulphide exchange with at least three different protein thiols of decreasing reactivity. The first is associated with Mg2(+)-dependent activation, the second is associated with a tonic inhibition of activity and the third is associated with the catalytic activity, although probably not at the active site. PMID:1673335

Catalytic oxidation of o-aminophenols and aromatic amines by mushroom tyrosinase.

PubMed

Muñoz-Muñoz, Jose Luis; Garcia-Molina, Francisco; Garcia-Ruiz, Pedro Antonio; Varon, Ramon; Tudela, Jose; Rodriguez-Lopez, Jose N; Garcia-Canovas, Francisco

2011-12-01

The kinetics of tyrosinase acting on o-aminophenols and aromatic amines as substrates was studied. The catalytic constants of aromatic monoamines and o-diamines were both low, these results are consistent with our previous mechanism in which the slow step is the transfer of a proton by a hydroxyl to the peroxide in oxy-tyrosinase (Fenoll et al., Biochem. J. 380 (2004) 643-650). In the case of o-aminophenols, the hydroxyl group indirectly cooperates in the transfer of the proton and consequently the catalytic constants in the action of tyrosinase on these compounds are higher. In the case of aromatic monoamines, the Michaelis constants are of the same order of magnitude than for monophenols, which suggests that the monophenols bind better (higher binding constant) to the enzyme to facilitate the π-π interactions between the aromatic ring and a possible histidine of the active site. In the case of aromatic o-diamines, both the catalytic and Michaelis constants are low, the values of the catalytic constants being lower than those of the corresponding o-diphenols. The values of the Michaelis constants of the aromatic o-diamines are slightly lower than those of their corresponding o-diphenols, confirming that the aromatic o-diamines bind less well (lower binding constant) to the enzyme. Copyright © 2011 Elsevier B.V. All rights reserved.

De Novo Genome Project for the Aromatic Degrader Rhodococcus pyridinivorans Strain AK37

PubMed Central

Kriszt, Balázs; Táncsics, András; Cserháti, Mátyás; Tóth, Ákos; Nagy, István; Horváth, Balázs; Nagy, István; Tamura, Tomohiro; Szoboszlay, Sándor

2012-01-01

Here, we present the complete genome sequence of Rhodococcus pyridinivorans AK37 strain NCAIM PB1376, which was isolated from an oil-polluted site in Hungary. R. pyridinivorans AK37 is an aerobic, nonsporulating, nonmotile, Gram-positive bacterium with remarkable aromatic-decomposing activity. PMID:22328750

Detecting the building blocks of aromatics

NASA Astrophysics Data System (ADS)

Joblin, Christine; Cernicharo, José

2018-01-01

Interstellar clouds are sites of active organic chemistry (1). Many small, gasphase molecules are found in the dark parts of the clouds that are protected from ultraviolet (UV) photons, but these molecules photodissociate in the external layers of the cloud that are exposed to stellar radiation (see the photo). These irradiated regions are populated by large polycyclic aromatic hydrocarbons (PAHs) with characteristic infrared (IR) emission features. These large aromatics are expected to form from benzene (C6H6), which is, however, difficult to detect because it does not have a permanent dipole moment and can only be detected via its IR absorption transitions against a strong background source (2). On page 202 of this issue, McGuire et al. (3) report the detection of benzonitrile (c-C6H5CN) with radio telescopes. Benzonitrile likely forms in the reaction of CN with benzene; from its observation, it is therefore possible to estimate the abundance of benzene itself.

Dehalogenation of aromatics by nucleophilic aromatic substitution.

PubMed

Sadowsky, Daniel; McNeill, Kristopher; Cramer, Christopher J

2014-09-16

Nucleophilic aromatic substitution has been implicated as a mechanism for both the biotic and abiotic hydrodehalogenation of aromatics. Two mechanisms for the aqueous dehalogenation of aromatics involving nucleophilic aromatic substitution with hydride as a nucleophile are investigated using a validated density functional and continuum solvation protocol. For chlorinated and brominated aromatics, nucleophilic addition ortho to carbon-halogen bonds via an anionic intermediate is predicted to be the preferred mechanism in the majority of cases, while concerted substitution is predicted to be preferred for most fluorinated aromatics. Nucleophilic aromatic substitution reactions with the hydroxide and hydrosulfide anions as nucleophiles are also investigated and compared.

Breaking Benzene Aromaticity-Computational Insights into the Mechanism of the Tungsten-Containing Benzoyl-CoA Reductase.

PubMed

Culka, Martin; Huwiler, Simona G; Boll, Matthias; Ullmann, G Matthias

2017-10-18

Aromatic compounds are environmental pollutants with toxic and carcinogenic properties. Despite the stability of aromatic rings, bacteria are able to degrade the aromatic compounds into simple metabolites and use them as growth substrates under oxic or even under anoxic conditions. In anaerobic microorganisms, most monocyclic aromatic growth substrates are converted to the central intermediate benzoyl-coenzyme A, which is enzymatically reduced to cyclohexa-1,5-dienoyl-CoA. The strictly anaerobic bacterium Geobacter metallireducens uses the class II benzoyl-CoA reductase complex for this reaction. The catalytic BamB subunit of this complex harbors an active site tungsten-bis-pyranopterin cofactor with the metal being coordinated by five protein/cofactor-derived sulfur atoms and a sixth, so far unknown, ligand. Although BamB has been biochemically and structurally characterized, its mechanism still remains elusive. Here we use continuum electrostatic and QM/MM calculations to model benzoyl-CoA reduction by BamB. We aim to elucidate the identity of the sixth ligand of the active-site tungsten ion together with the interplay of the electron and proton transfer events during the aromatic ring reduction. On the basis of our calculations, we propose that benzoyl-CoA reduction is initiated by a hydrogen atom transfer from a W(IV) species with an aqua ligand, yielding W(V)-[OH - ] and a substrate radical intermediate. In the next step, a proton-assisted second electron transfer takes place with a conserved active-site histidine serving as the second proton donor. Interestingly, our calculations suggest that the electron for the second reduction step is taken from the pyranopterin cofactors rather than from the tungsten ion. The resulting cationic radical, which is distributed over both pyranopterins, is stabilized by conserved anionic amino acid residues. The stepwise mechanism of the reduction shows similarities to the Birch reduction known from organic chemistry. However

Structure-Activity Relationships for Rates of Aromatic Amine Oxidation by Manganese Dioxide.

PubMed

Salter-Blanc, Alexandra J; Bylaska, Eric J; Lyon, Molly A; Ness, Stuart C; Tratnyek, Paul G

2016-05-17

New energetic compounds are designed to minimize their potential environmental impacts, which includes their transformation and the fate and effects of their transformation products. The nitro groups of energetic compounds are readily reduced to amines, and the resulting aromatic amines are subject to oxidation and coupling reactions. Manganese dioxide (MnO2) is a common environmental oxidant and model system for kinetic studies of aromatic amine oxidation. In this study, a training set of new and previously reported kinetic data for the oxidation of model and energetic-derived aromatic amines was assembled and subjected to correlation analysis against descriptor variables that ranged from general purpose [Hammett σ constants (σ(-)), pKas of the amines, and energies of the highest occupied molecular orbital (EHOMO)] to specific for the likely rate-limiting step [one-electron oxidation potentials (Eox)]. The selection of calculated descriptors (pKa, EHOMO, and Eox) was based on validation with experimental data. All of the correlations gave satisfactory quantitative structure-activity relationships (QSARs), but they improved with the specificity of the descriptor. The scope of correlation analysis was extended beyond MnO2 to include literature data on aromatic amine oxidation by other environmentally relevant oxidants (ozone, chlorine dioxide, and phosphate and carbonate radicals) by correlating relative rate constants (normalized to 4-chloroaniline) to EHOMO (calculated with a modest level of theory).

Polycyclic Aromatic Hydrocarbons: A Critical Review of Environmental Occurrence and Bioremediation.

PubMed

Alegbeleye, Oluwadara Oluwaseun; Opeolu, Beatrice Oluwatoyin; Jackson, Vanessa Angela

2017-10-01

The degree of polycyclic aromatic hydrocarbon contamination of environmental matrices has increased over the last several years due to increase in industrial activities. Interest has surrounded the occurrence and distribution of polycyclic aromatic hydrocarbons for many decades because they pose a serious threat to the health of humans and ecosystems. The importance of the need for sustainable abatement strategies to alleviate contamination therefore cannot be overemphasised, as daily human activities continue to create pollution from polycyclic aromatic hydrocarbons and impact the natural environment. Globally, attempts have been made to design treatment schemes for the remediation and restoration of contaminated sites. Several techniques and technologies have been proposed and tested over time, the majority of which have significant limitations. This has necessitated research into environmentally friendly and cost-effective clean-up techniques. Bioremediation is an appealing option that has been extensively researched and adopted as it has been proven to be relatively cost-effective, environmentally friendly and is publicly accepted. In this review, the physicochemical properties of some priority polycyclic aromatic hydrocarbons, as well as the pathways and mechanisms through which they enter the soil, river systems, drinking water, groundwater and food are succinctly examined. Their effects on human health, other living organisms, the aquatic ecosystem, as well as soil microbiota are also elucidated. The persistence and bioavailability of polycyclic aromatic hydrocarbons are discussed as well, as they are important factors that influence the rate, efficiency and overall success of remediation. Bioremediation (aerobic and anaerobic), use of biosurfactants and bioreactors, as well as the roles of biofilms in the biological treatment of polycyclic aromatic hydrocarbons are also explored.

Polycyclic Aromatic Hydrocarbons: A Critical Review of Environmental Occurrence and Bioremediation

NASA Astrophysics Data System (ADS)

Alegbeleye, Oluwadara Oluwaseun; Opeolu, Beatrice Oluwatoyin; Jackson, Vanessa Angela

2017-10-01

The degree of polycyclic aromatic hydrocarbon contamination of environmental matrices has increased over the last several years due to increase in industrial activities. Interest has surrounded the occurrence and distribution of polycyclic aromatic hydrocarbons for many decades because they pose a serious threat to the health of humans and ecosystems. The importance of the need for sustainable abatement strategies to alleviate contamination therefore cannot be overemphasised, as daily human activities continue to create pollution from polycyclic aromatic hydrocarbons and impact the natural environment. Globally, attempts have been made to design treatment schemes for the remediation and restoration of contaminated sites. Several techniques and technologies have been proposed and tested over time, the majority of which have significant limitations. This has necessitated research into environmentally friendly and cost-effective clean-up techniques. Bioremediation is an appealing option that has been extensively researched and adopted as it has been proven to be relatively cost-effective, environmentally friendly and is publicly accepted. In this review, the physicochemical properties of some priority polycyclic aromatic hydrocarbons, as well as the pathways and mechanisms through which they enter the soil, river systems, drinking water, groundwater and food are succinctly examined. Their effects on human health, other living organisms, the aquatic ecosystem, as well as soil microbiota are also elucidated. The persistence and bioavailability of polycyclic aromatic hydrocarbons are discussed as well, as they are important factors that influence the rate, efficiency and overall success of remediation. Bioremediation (aerobic and anaerobic), use of biosurfactants and bioreactors, as well as the roles of biofilms in the biological treatment of polycyclic aromatic hydrocarbons are also explored.

Quantifying reactivity for electrophilic aromatic substitution reactions with Hirshfeld charge.

PubMed

Liu, Shubin

2015-03-26

An electrophilic aromatic substitution is a process where one atom or group on an aromatic ring is replaced by an incoming electrophile. The reactivity and regioselectivity of this category of reactions is significantly impacted by the group that is already attached to the aromatic ring. Groups promoting substitution at the ortho/para and meta position are called ortho/para and meta directing groups, respectively. Earlier, we have shown that regioselectivity of the electrophilic aromatic substitution is dictated by the nucleophilicity of the substituted aromatic ring, which is proportional to the Hirshfeld charge on the regioselective site. Ortho/para directing groups have the largest negative charge values at the ortho/para positions, whereas meta directing groups often have the largest negative charge value at the meta position. The electron donation or acceptance feature of a substitution group is irrelevant to the regioselectivity. In this contribution, we extend our previous study by quantifying the reactivity for this kind of reactions. To that end, we examine the transition-state structure and activation energy of an identity reaction for a series of monosubstituted-benzene molecules reacting with hydrogen fluoride using BF3 as the catalyst in the gas phase. A total of 18 substitution groups will be considered, nine of which are ortho/para directing and the other nine groups meta directing. From this study, we found that the barrier height of these reactions strongly correlates with the Hirshfeld charge on the regioselective site for both ortho/para and meta directing groups, with the correlation coefficient R(2) both better than 0.96. We also discovered a less accurate correlation between the barrier height and HOMO energy. These results reconfirm the validity and effectiveness of employing the Hirshfeld charge as a reliable descriptor of both reactivity and regioselectivity for this vastly important category of chemical transformations.

Tailoring ZSM-5 Zeolites for the Fast Pyrolysis of Biomass to Aromatic Hydrocarbons.

PubMed

Hoff, Thomas C; Gardner, David W; Thilakaratne, Rajeeva; Wang, Kaige; Hansen, Thomas W; Brown, Robert C; Tessonnier, Jean-Philippe

2016-06-22

The production of aromatic hydrocarbons from cellulose by zeolite-catalyzed fast pyrolysis involves a complex reaction network sensitive to the zeolite structure, crystallinity, elemental composition, porosity, and acidity. The interplay of these parameters under the reaction conditions represents a major roadblock that has hampered significant improvement in catalyst design for over a decade. Here, we studied commercial and laboratory-synthesized ZSM-5 zeolites and combined data from 10 complementary characterization techniques in an attempt to identify parameters common to high-performance catalysts. Crystallinity and framework aluminum site accessibility were found to be critical to achieve high aromatic yields. These findings enabled us to synthesize a ZSM-5 catalyst with enhanced activity, which offers the highest aromatic hydrocarbon yield reported to date. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Co-aromatization of olefin and methane over Ag-Ga/ZSM-5 catalyst at low temperature

DOE Office of Scientific and Technical Information (OSTI.GOV)

He, Peng; Gatip, Richard; Yung, Matthew

The massive exploitation of shale gas in the past decade has boosted the production of natural gas and reduced its price dramatically. The methane activation and following conversion into more valuable fuels and chemicals have thus become more and more attractive, while the introduction of hydrocarbons to enhance the methane activation at mild conditions represents a promising approach. In the present work, the co-aromatization of methane with propylene has been studied at 400 °C. The presence of methane would increase the toluene to benzene ratio as well as the average carbon number of the formed liquid aromatic products compared tomore » its propylene alone counterpart. Among the gas products, the formations of C 3H 8, C 4H 8 and C 4H 10 also get promoted when methane is present. The incorporation of methane into the product molecules is also directly evidenced by the 1H, 2D and 13C NMR spectroscopy of the liquid products obtained from the reaction between propylene (or styrene) and isotope labelled methane. Hydrogen from methane would contribute a large portion of the hydrogen in the product molecules, while the benzylic and aromatic hydrogen sites are favored compared with those on the alkyl side chains. The activation of methane is also observed in the DRIFT spectra when deuterium enriched methane is engaged as the methane source and evidenced by the escalated exothermic feature when olefin aromatization takes place under methane environment. The excellent catalytic performance of Ag-Ga/ZSM-5 might be because of the better dispersion of Ag and Ga on the ZSM-5 surface and moderate amount of strong Brosted and Lewis surface acid sites. All the observations suggest that methane might be activated nonoxidatively and converted into aromatics if suitable catalyst is charged under the assistance of co-existing olefin. In conclusion, the reported synergetic effect could potentially lead to the more economic utilization of abundant natural gas and petrochemical

Co-aromatization of olefin and methane over Ag-Ga/ZSM-5 catalyst at low temperature

DOE PAGES

He, Peng; Gatip, Richard; Yung, Matthew; ...

2017-04-22

The massive exploitation of shale gas in the past decade has boosted the production of natural gas and reduced its price dramatically. The methane activation and following conversion into more valuable fuels and chemicals have thus become more and more attractive, while the introduction of hydrocarbons to enhance the methane activation at mild conditions represents a promising approach. In the present work, the co-aromatization of methane with propylene has been studied at 400 °C. The presence of methane would increase the toluene to benzene ratio as well as the average carbon number of the formed liquid aromatic products compared tomore » its propylene alone counterpart. Among the gas products, the formations of C 3H 8, C 4H 8 and C 4H 10 also get promoted when methane is present. The incorporation of methane into the product molecules is also directly evidenced by the 1H, 2D and 13C NMR spectroscopy of the liquid products obtained from the reaction between propylene (or styrene) and isotope labelled methane. Hydrogen from methane would contribute a large portion of the hydrogen in the product molecules, while the benzylic and aromatic hydrogen sites are favored compared with those on the alkyl side chains. The activation of methane is also observed in the DRIFT spectra when deuterium enriched methane is engaged as the methane source and evidenced by the escalated exothermic feature when olefin aromatization takes place under methane environment. The excellent catalytic performance of Ag-Ga/ZSM-5 might be because of the better dispersion of Ag and Ga on the ZSM-5 surface and moderate amount of strong Brosted and Lewis surface acid sites. All the observations suggest that methane might be activated nonoxidatively and converted into aromatics if suitable catalyst is charged under the assistance of co-existing olefin. In conclusion, the reported synergetic effect could potentially lead to the more economic utilization of abundant natural gas and petrochemical

Structure-Activity Relationships for Rates of Aromatic Amine Oxidation by Manganese Dioxide

DOE PAGES

Salter-Blanc, Alexandra J.; Bylaska, Eric J.; Lyon, Molly A.; ...

2016-04-13

New energetic compounds are designed to minimize their potential environmental impacts, which includes their transformation and the fate and effects of their transformation products. The nitro groups of energetic compounds are readily reduced to amines, and the resulting aromatic amines are subject to oxidation and coupling reactions. Manganese dioxide (MnO 2) is a common environmental oxidant and model system for kinetic studies of aromatic amine oxidation. Here in this study, a training set of new and previously reported kinetic data for the oxidation of model and energetic-derived aromatic amines was assembled and subjected to correlation analysis against descriptor variables that ranged from general purpose [Hammettmore » $$\\sigma$$ constants ($$\\sigma^-$$), pK as of the amines, and energies of the highest occupied molecular orbital (E HOMO)] to specific for the likely rate-limiting step [one-electron oxidation potentials (E ox)]. The selection of calculated descriptors (pK a), E HOMO, and E ox) was based on validation with experimental data. All of the correlations gave satisfactory quantitative structure-activity relationships (QSARs), but they improved with the specificity of the descriptor. The scope of correlation analysis was extended beyond MnO 2 to include literature data on aromatic amine oxidation by other environmentally relevant oxidants (ozone, chlorine dioxide, and phosphate and carbonate radicals) by correlating relative rate constants (normalized to 4-chloroaniline) to E HOMO (calculated with a modest level of theory).« less

Structure-Activity Relationships for Rates of Aromatic Amine Oxidation by Manganese Dioxide

DOE Office of Scientific and Technical Information (OSTI.GOV)

Salter-Blanc, Alexandra J.; Bylaska, Eric J.; Lyon, Molly A.

New energetic compounds are designed to minimize their potential environmental impacts, which includes their transformation and the fate and effects of their transformation products. The nitro groups of energetic compounds are readily reduced to amines, and the resulting aromatic amines are subject to oxidation and coupling reactions. Manganese dioxide (MnO 2) is a common environmental oxidant and model system for kinetic studies of aromatic amine oxidation. Here in this study, a training set of new and previously reported kinetic data for the oxidation of model and energetic-derived aromatic amines was assembled and subjected to correlation analysis against descriptor variables that ranged from general purpose [Hammettmore » $$\\sigma$$ constants ($$\\sigma^-$$), pK as of the amines, and energies of the highest occupied molecular orbital (E HOMO)] to specific for the likely rate-limiting step [one-electron oxidation potentials (E ox)]. The selection of calculated descriptors (pK a), E HOMO, and E ox) was based on validation with experimental data. All of the correlations gave satisfactory quantitative structure-activity relationships (QSARs), but they improved with the specificity of the descriptor. The scope of correlation analysis was extended beyond MnO 2 to include literature data on aromatic amine oxidation by other environmentally relevant oxidants (ozone, chlorine dioxide, and phosphate and carbonate radicals) by correlating relative rate constants (normalized to 4-chloroaniline) to E HOMO (calculated with a modest level of theory).« less

Carbohydrate–Aromatic Interactions in Proteins

PubMed Central

2015-01-01

Protein–carbohydrate interactions play pivotal roles in health and disease. However, defining and manipulating these interactions has been hindered by an incomplete understanding of the underlying fundamental forces. To elucidate common and discriminating features in carbohydrate recognition, we have analyzed quantitatively X-ray crystal structures of proteins with noncovalently bound carbohydrates. Within the carbohydrate-binding pockets, aliphatic hydrophobic residues are disfavored, whereas aromatic side chains are enriched. The greatest preference is for tryptophan with an increased prevalence of 9-fold. Variations in the spatial orientation of amino acids around different monosaccharides indicate specific carbohydrate C–H bonds interact preferentially with aromatic residues. These preferences are consistent with the electronic properties of both the carbohydrate C–H bonds and the aromatic residues. Those carbohydrates that present patches of electropositive saccharide C–H bonds engage more often in CH−π interactions involving electron-rich aromatic partners. These electronic effects are also manifested when carbohydrate–aromatic interactions are monitored in solution: NMR analysis indicates that indole favorably binds to electron-poor C–H bonds of model carbohydrates, and a clear linear free energy relationships with substituted indoles supports the importance of complementary electronic effects in driving protein–carbohydrate interactions. Together, our data indicate that electrostatic and electronic complementarity between carbohydrates and aromatic residues play key roles in driving protein–carbohydrate complexation. Moreover, these weak noncovalent interactions influence which saccharide residues bind to proteins, and how they are positioned within carbohydrate-binding sites. PMID:26561965

Carbohydrate-Aromatic Interactions in Proteins.

PubMed

Hudson, Kieran L; Bartlett, Gail J; Diehl, Roger C; Agirre, Jon; Gallagher, Timothy; Kiessling, Laura L; Woolfson, Derek N

2015-12-09

Protein-carbohydrate interactions play pivotal roles in health and disease. However, defining and manipulating these interactions has been hindered by an incomplete understanding of the underlying fundamental forces. To elucidate common and discriminating features in carbohydrate recognition, we have analyzed quantitatively X-ray crystal structures of proteins with noncovalently bound carbohydrates. Within the carbohydrate-binding pockets, aliphatic hydrophobic residues are disfavored, whereas aromatic side chains are enriched. The greatest preference is for tryptophan with an increased prevalence of 9-fold. Variations in the spatial orientation of amino acids around different monosaccharides indicate specific carbohydrate C-H bonds interact preferentially with aromatic residues. These preferences are consistent with the electronic properties of both the carbohydrate C-H bonds and the aromatic residues. Those carbohydrates that present patches of electropositive saccharide C-H bonds engage more often in CH-π interactions involving electron-rich aromatic partners. These electronic effects are also manifested when carbohydrate-aromatic interactions are monitored in solution: NMR analysis indicates that indole favorably binds to electron-poor C-H bonds of model carbohydrates, and a clear linear free energy relationships with substituted indoles supports the importance of complementary electronic effects in driving protein-carbohydrate interactions. Together, our data indicate that electrostatic and electronic complementarity between carbohydrates and aromatic residues play key roles in driving protein-carbohydrate complexation. Moreover, these weak noncovalent interactions influence which saccharide residues bind to proteins, and how they are positioned within carbohydrate-binding sites.

Critical Amino Acids in the Active Site of Meprin Metalloproteinases for Substrate and Peptide Bond Specificity*

PubMed Central

Villa, James P.; Bertenshaw, Greg P.; Bond, Judith S.

2008-01-01

SUMMARY The protease domains of the evolutionarily-related α and ß subunits of meprin metalloproteases are approximately 55% identical at the amino acid level, however, their substrate and peptide bond specificities differ markedly. The meprin ß subunit favors acidic residues proximal to the scissile bond, while the α subunit prefers small or aromatic amino acids flanking the scissile bond. Thus gastrin, a peptide that contains a string of five Glu residues, is an excellent substrate for meprin ß while it is not hydrolyzed by meprin α. Work herein aimed to identify critical amino acids in the meprin active sites that determine the substrate specificity differences. Sequence alignments and homology models, based on the crystal structure of the crayfish astacin, showed electrostatic differences within the meprin active sites. Site-directed mutagenesis of active site residues demonstrated that replacement of a hydrophobic residue by a basic amino acid enabled the meprin α protease to cleave gastrin. The meprin αY199K mutant was most effective; the corresponding mutation of meprin ßK185Y resulted in decreased activity toward gastrin. Peptide cleavage site determinations and kinetic analyses using a variety of peptides extended evidence that meprin αTyr199/ßLys185 are substrate specificity determinants in meprin active sites. These studies shed light on the molecular basis for the substrate specificity differences of astacin metalloproteinases. PMID:12888571

Characterization of the oestrogenic activity of non-aromatic steroids: are there male-specific endogenous oestrogen receptor modulators?

PubMed Central

Wang, Pan; Wen, Yujing; Han, Gui-Zhen; Sidhu, Pritam Kaur; Zhu, Bao Ting

2009-01-01

Background and purpose: The endogenous oestrogens have important biological functions in men as well as in women. Because 17β-oestradiol and oestrone are also formed in the male body, these aromatic oestrogens are generally thought to be responsible for exerting the required oestrogenic functions in the male. In the present study, we tested the hypothesis that some of the non-aromatic steroids that are androgen precursors or metabolites with hydroxyl groups at C-3 and/or C-17 positions may also be able to serve as ligands for the oestrogen receptors (ER) in the male. Experimental approach: A total of sixty non-aromatic steroids (selected from families of androstens, androstans, androstadiens, oestrens and oestrans) were analysed for their ability to bind and activate the human ERα and ERβin vitro and in cultured cells. Key results: Six of the non-aromatic steroids, that is, 5-androsten-3β,17β-diol, 5α-androstan-3β,17β-diol, 5(10)-oestren-3α,17β-diol, 5(10)-oestren-3β,17β-diol, 4-oestren-3β,17β-diol and 5α-oestran-3β,17β-diol, were found to have physiologically relevant high binding affinity (∼50% of that of oestrone) for human ERα and ERβ. These non-aromatic steroids also activated the transcriptional activity of human ERs and elicited biological responses (such as growth stimulation) in two representative ER-positive human cancer cell lines (MCF-7 and LNCaP) with physiologically relevant potency and efficacy. Molecular docking analysis of these six active compounds showed that they could bind to ERα and ERβ in a manner similar to that of 17β-oestradiol. Conclusions and implications: These results provide evidence for the possibility that some of the endogenous androgen precursors or metabolites could serve as male-specific ER ligands. PMID:19888961

A quantum chemical study for exploring the inhibitory effect of nitrogen containing species on the adsorption of polynuclear aromatic hydrocarbons over a Bronsted acid site

NASA Astrophysics Data System (ADS)

Celis-Cornejo, C. M.; Garnica Mantilla, M. M.; Baldovino-Medrano, V. G.; Ramírez-Caballero, G. E.

2016-08-01

The analysis of the inhibitory effect of nitrogenated compounds on the hydroprocessing and hydropurification of oil derived fuels is important to produce cleaner fuels. In this work, density functional theory calculations were performed to investigate the effect of the nitrogen containing molecules on the adsorption of Polynuclear Aromatic Hydrocarbons (PAHs). Mordenite was chosen as a zeolitic structure for simulating a Bronsted acid site. The character of the acid site was confirmed by both a vibrational frequency calculation and a Bader charge analysis. From the adsorption calculations, it was found that the adsorption energy of PAHs increases with the number of aromatic rings in the structure. Also, the nitrogen containing species possibly inhibit more extensively two and three rings PAHs because of their lower adsorption energies. Finally, it was observed that the nitrogen species tend to drag the proton from the mordenite acid site. This explains the inhibitory effect in the adsorption of PAHs and contributes to understanding the dynamics of hydrocarbon hydroprocessing in refineries.

Analysis of polycyclic aromatic hydrocarbons in tree-rings of Masson pine (Pinus massoniana L.) from two industrial sites in the Pearl River Delta, south China.

PubMed

Kuang, Yuan-wen; Zhou, Guo-yi; Wen, Da-zhi; Li, Jiong; Sun, Fang-fang

2011-09-01

Concentrations of polycyclic aromatic hydrocarbons (PAHs) were examined and potential sources of PAHs were identified from the dated tree-rings of Masson pine (Pinus massoniana L.) near two industrial sites (Danshuikeng, DSK and Xiqiaoshan, XQS) in the Pearl River Delta of south China. Total concentrations of PAHs (∑PAHs) were revealed with similar patterns of temporal trends in the tree-rings at both sites, suggesting tree-rings recorded the historical variation in atmospheric PAHs. The differences of individual PAHs and of ∑PAHs detected in the tree-rings between the two sites reflected the historical differences of airborne PAHs. Regional changes in industrial activities might contribute to the site-specific and period-specific patterns of the tree-ring PAHs. The diagnostic PAH ratios of Ant/(Ant + PA), FL/(FL + Pyr), and BaA/(BaA + Chr)) revealed that PAHs in the tree-rings at both sites mainly stemmed from the combustion process (pyrogenic sources). Principal component analysis further confirmed that wood burning, coal combustion, diesel, and gasoline-powered vehicular emissions were the dominant contributors of PAHs sources at DSK, while diesel combustion, gasoline and natural gas combustion, and incomplete coal combustion were responsible for the main origins of PAHs at XQS. Tree-ring analysis of PAHs was indicative of PAHs from a mixture of sources of combustion, thus minimizing the bias of short-term active air sampling.

Characterization of an aryl-alcohol oxidase from the plant saprophytic basidiomycete Coprinopsis cinerea with broad substrate specificity against aromatic alcohols.

PubMed

Tamaru, Yoshiaki; Umezawa, Kiwamu; Yoshida, Makoto

2018-07-01

The aim of the study was to obtain information about the enzymatic properties of aryl-alcohol oxidase from the plant saprophytic basidiomycete Coprinopsis cinerea (rCcAAO), which is classified into the auxiliary activities family 3 subfamily 2 (AA3_2). The gene encoding AAO from the plant saprophytic basidiomycete Coprinopsis cinerea (CcAAO) was cloned, and the recombinant CcAAO (rCcAAO) was heterologously expressed in the methylotrophic yeast Pichia pastoris. The purified rCcAAO showed significant activity not only against trans,trans-2,4-hexadien-1-ol but also against a broad range of aromatic alcohols including aromatic compounds that were reported to be poor substrates for known AAOs. Moreover, site-directed mutagenesis analysis demonstrated that mutants with substitutions from leucine to phenylalanine and tryptophan at position 416 exhibited decreases of activity for aromatic alcohols but still maintained the activity for trans,trans-2,4-hexadien-1-ol. Leucine 416 in CcAAO contributes to the broad substrate specificity against various aromatic alcohols, which is useful for the production of hydrogen peroxide using this enzyme.

Characterization of TSP-bound n-alkanes and polycyclic aromatic hydrocarbons at rural and urban sites of Tianjin, China.

PubMed

Wu, Shui-Ping; Tao, Shu; Zhang, Zhi-Huan; Lan, Tian; Zuo, Qian

2007-05-01

Total suspended particle (TSP) was collected and analyzed at rural and urban sites in Tianjin, China during the domestic heating season (from 15 November to 15 March) of 2003/4 for n-alkanes and 16 polycyclic aromatic hydrocarbons (PAHs). The normalized distribution of n-alkanes with the peak at C22, C23, C24 or C25 suggested that fossil fuel utilization was the major source of particulate n-alkanes at both sites. PAHs normalized distribution for each sample was similar and the higher molecular weight PAH dominated the profile (around 90%) indicating a stronger combustion source at both sites. Precipitation and wind were the most important meteorological factors influencing TSP and PAHs atmospheric concentrations. In the urban area the emission height had significant influence on PAHs levels at different heights under the relative stable atmospheric conditions. Coal combustion was the major source for TSP-bound PAHs at both sites based on some diagnostic ratios.

Structural analysis of substrate-mimicking inhibitors in complex with Neisseria meningitidis 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase - The importance of accommodating the active site water.

PubMed

Heyes, Logan C; Reichau, Sebastian; Cross, Penelope J; Jameson, Geoffrey B; Parker, Emily J

2014-12-01

3-Deoxy-d-arabino-heptulosonate 7-phosphate synthase (DAH7PS) catalyses the first committed step of the shikimate pathway, which produces the aromatic amino acids as well as many other aromatic metabolites. DAH7PS catalyses an aldol-like reaction between phosphoenolpyruvate and erythrose 4-phosphate. Three phosphoenolpyruvate mimics, (R)-phospholactate, (S)-phospholactate and vinyl phosphonate [(E)-2-methyl-3-phosphonoacrylate], were found to competitively inhibit DAH7PS from Neisseria meningitidis, which is the pathogen responsible for bacterial meningitis. The most potent inhibitor was the vinyl phosphonate with a Ki value of 3.9±0.4μM. We report for the first time crystal structures of these compounds bound in the active site of a DAH7PS enzyme which reveals that the inhibitors bind to the active site of the enzyme in binding modes that mimic those of the predicted oxocarbenium and tetrahedral intermediates of the enzyme-catalysed reaction. Furthermore, the inhibitors accommodate the binding of a key active site water molecule. Together, these observations provide strong evidence that this active site water participates directly in the DAH7PS reaction, enabling the facial selectivity of the enzyme-catalysed reaction sequence to be delineated. Copyright © 2014 Elsevier Inc. All rights reserved.

Cation Radical Accelerated Nucleophilic Aromatic Substitution via Organic Photoredox Catalysis.

PubMed

Tay, Nicholas E S; Nicewicz, David A

2017-11-15

Nucleophilic aromatic substitution (S N Ar) is a direct method for arene functionalization; however, it can be hampered by low reactivity of arene substrates and their availability. Herein we describe a cation radical-accelerated nucleophilic aromatic substitution using methoxy- and benzyloxy-groups as nucleofuges. In particular, lignin-derived aromatics containing guaiacol and veratrole motifs were competent substrates for functionalization. We also demonstrate an example of site-selective substitutive oxygenation with trifluoroethanol to afford the desired trifluoromethylaryl ether.

Magnesium-adenosine diphosphate binding sites in wild-type creatine kinase and in mutants: role of aromatic residues probed by Raman and infrared spectroscopies.

PubMed

Hagemann, H; Marcillat, O; Buchet, R; Vial, C

2000-08-08

Two distinct methods were used to investigate the role of Trp residues during Mg-ADP binding to cytosolic creatine kinase (CK) from rabbit muscle: (1) Raman spectroscopy, which is very sensitive to the environment of aromatic side-chain residues, and (2) reaction-induced infrared difference spectroscopy (RIDS) and photolabile substrate (ADP[Et(PhNO(2))]), combined with site-directed mutagenesis on the four Trp residues of CK. Our Raman results indicated that the environment of Trp and of Tyr were not affected during Mg-ADP binding to CK. Analysis of RIDS of wild-type CK, inactive W227Y, and active W210,217,272Y mutants suggested that Trp227 was not involved in the stacking interactions. Results are consistent with Trp227 being essential to prevent water molecules from entering in the active site [as suggested by Gross, M., Furter-Graves, E. M., Wallimann, T., Eppenberger, H. M., and Furter, R. (1994) Protein Sci. 3, 1058-1068] and that another Trp could in addition help to steer the nucleotide in the binding site, although it is not essential for the activity of CK. Raman and infrared spectra indicated that Mg-ADP binding does not involve large secondary structure changes. Only 3-4 residues absorbing in the amide I region are directly implicated in the Mg-ADP binding (corresponding to secondary structure changes less than 1%), suggesting that movement of protein domains due to Mg-nucleotide binding do not promote large secondary structure changes.

Availability of polycyclic aromatic hydrocarbons from lampblack-impacted soils at former oil-gas plant sites in California, USA.

PubMed

Hong, Lei; Luthy, Richard G

2007-03-01

Lampblack-impacted soils at former oil-gas plant sites in California, USA, were characterized to assess the sorption of polycyclic aromatic hydrocarbons (PAHs) and the concentration-dependent effects of a residual oil tar phase on sorption mechanism and availability of PAHs. Nuclear magnetic resonance spectroscopy demonstrated similar aromaticity for both lampblack carbon and the oil tar phase, with pronounced resonance signals in the range of 100 to 150 ppm. Scanning-electron microscopic images revealed a physically distinct oil tar phase, especially at high concentrations in lampblack, which resulted in an organic-like film structure when lampblack particles became saturated with the oil tar. Sorption experiments were conducted on a series of laboratory-prepared lampblack samples to systematically evaluate influences of an oil tar phase on PAH sorption to lampblack. Results indicate that the sorption of PAHs to lampblack exhibits a competition among sorption phases at low oil tar contents when micro- and mesopores are accessible. When the oil tar content increases to more than 5 to 10% by weight, this tar phase fills small pores, reduces surface area, and dominates PAH sorption on lampblack surface. A new PAH partitioning model, Kd = KLB-C(1 - ftar)alpha + ftarKtar (alpha = empirical exponent), incorporates these effects in which the control of PAH partitioning transits from being dominated by sorption in lampblack (KLB-C) to absorption in oil tar (Ktar), depending on the fraction of tar (ftar). This study illustrates the importance of understanding interactions among PAHs, oil tar, and lampblack for explaining the differences in availability of PAHs among site soils and, consequently, for refining site-specific risk assessment and establishing soil cleanup levels.

One-step hydroprocessing of fatty acids into renewable aromatic hydrocarbons over Ni/HZSM-5: insights into the major reaction pathways.

PubMed

Xing, Shiyou; Lv, Pengmei; Wang, Jiayan; Fu, Junying; Fan, Pei; Yang, Lingmei; Yang, Gaixiu; Yuan, Zhenhong; Chen, Yong

2017-01-25

For high caloricity and stability in bio-aviation fuels, a certain content of aromatic hydrocarbons (AHCs, 8-25 wt%) is crucial. Fatty acids, obtained from waste or inedible oils, are a renewable and economic feedstock for AHC production. Considerable amounts of AHCs, up to 64.61 wt%, were produced through the one-step hydroprocessing of fatty acids over Ni/HZSM-5 catalysts. Hydrogenation, hydrocracking, and aromatization constituted the principal AHC formation processes. At a lower temperature, fatty acids were first hydrosaturated and then hydrodeoxygenated at metal sites to form long-chain hydrocarbons. Alternatively, the unsaturated fatty acids could be directly deoxygenated at acid sites without first being saturated. The long-chain hydrocarbons were cracked into gases such as ethane, propane, and C 6 -C 8 olefins over the catalysts' Brønsted acid sites; these underwent Diels-Alder reactions on the catalysts' Lewis acid sites to form AHCs. C 6 -C 8 olefins were determined as critical intermediates for AHC formation. As the Ni content in the catalyst increased, the Brønsted-acid site density was reduced due to coverage by the metal nanoparticles. Good performance was achieved with a loading of 10 wt% Ni, where the Ni nanoparticles exhibited a polyhedral morphology which exposed more active sites for aromatization.

Poly(1,3,4-oxadiazoles) via aromatic nucleophilic displacement

NASA Technical Reports Server (NTRS)

Connell, John W. (Inventor); Hergenrother, Paul M. (Inventor); Wolf, Peter (Inventor)

1992-01-01

Poly(1,3,4-oxadiazoles) (POX) are prepared by the aromatic nucleophilic displacement reaction of di(hydroxyphenyl) 1,3,4-oxadiazole monomers with activated aromatic dihalides or activated aromatic dinitro compounds. The polymerizations are carried out in polar aprotic solvents such as sulfolane or diphenylsulfone using alkali metal bases such as potassium carbonate at elevated temperatures under nitrogen. The di(hydroxyphenyl) 1,3,4-oxadiazole monomers are synthesized by reacting 4-hydroxybenzoic hydrazide with phenyl 4-hydrobenzoate in the melt and also by reacting aromatic dihydrazides with two moles of phenyl 4-hydroxybenzoate in the melt. This synthetic route has provided high molecular weight POX of new chemical structure, is economically and synthetically more favorable than other routes, and allows for facile chemical structure variation due to the large variety of activated aromatic dihalides which are available.

Microbial diversity and activity of an aged soil contaminated by polycyclic aromatic hydrocarbons.

PubMed

Zhao, Xiaohui; Fan, Fuqiang; Zhou, Huaidong; Zhang, Panwei; Zhao, Gaofeng

2018-06-01

In-depth understanding of indigenous microbial assemblages resulted from aged contamination by polycyclic aromatic hydrocarbons (PAHs) is of vital importance in successful in situ bioremediation treatments. Soil samples of three boreholes were collected at 12 different vertical depths. Overall, the dominating three-ring PAHs (76.2%) were closely related to distribution patterns of soil dehydrogenase activity, microbial cell numbers, and Shannon biodiversity index (H') of indigenous microorganisms. High-molecular-weight PAHs tend to yield more diverse communities. Results from 16S rRNA analysis indicated that possible functional groups of PAH degradation include three species in Bacillus cereus group, Bacillus sp. SA Ant14, Nocardioides sp., and Ralstonia pickettii. Principal component analysis indicates significant positive correlations between the content of high-molecular-weight PAHs and the distribution of Bacillus weihenstephanensis KBAB4 and Nocardioides sp. The species B. cereus 03BB102, Bacillus thuringiensis, B. weihenstephanensis KBAB4, and Nocardioides sp. were recognized as main PAH degraders and thus recommended to be utilized in further bioremediation applications. The vertical distribution characteristics of PAHs in soil profiles (1-12 m) and the internal relationship between the transport mechanisms of PAHs and the response of soil biological properties help further understand the microbial diversity and activity in an aged site.

Active Site Desolvation and Thermostability Trade-Offs in the Evolution of Catalytically Diverse Triazine Hydrolases.

PubMed

Sugrue, Elena; Carr, Paul D; Scott, Colin; Jackson, Colin J

2016-11-15

The desolvation of ionizable residues in the active sites of enzymes and the subsequent effects on catalysis and thermostability have been studied in model systems, yet little about how enzymes can naturally evolve to include active sites with highly reactive and desolvated charges is known. Variants of triazine hydrolase (TrzN) with significant differences in their active sites have been isolated from different bacterial strains: TrzN from Nocardioides sp. strain MTD22 contains a catalytic glutamate residue (Glu241) that is surrounded by hydrophobic and aromatic second-shell residues (Pro214 and Tyr215), whereas TrzN from Nocardioides sp. strain AN3 has a noncatalytic glutamine residue (Gln241) at an equivalent position, surrounded by hydrophilic residues (Thr214 and His215). To understand how and why these variants have evolved, a series of TrzN mutants were generated and characterized. These results show that desolvation by second-shell residues increases the pK a of Glu241, allowing it to act as a general acid at neutral pH. However, significant thermostability trade-offs are required to incorporate the ionizable Glu241 in the active site and to then enclose it in a hydrophobic microenvironment. Analysis of high-resolution crystal structures shows that there are almost no structural changes to the overall configuration of the active site due to these mutations, suggesting that the changes in activity and thermostability are purely based on the altered electrostatics. The natural evolution of these enzyme isoforms provides a unique system in which to study the fundamental process of charged residue desolvation in enzyme catalysis and its relative contribution to the creation and evolution of an enzyme active site.

Conserved tyrosine 182 residue in hyperthermophilic esterase EstE1 plays a critical role in stabilizing the active site.

PubMed

Truongvan, Ngoc; Chung, Hye-Shin; Jang, Sei-Heon; Lee, ChangWoo

2016-03-01

An aromatic amino acid, Tyr or Trp, located in the esterase active site wall, is highly conserved, with hyperthermophilic esterases showing preference for Tyr and lower temperature esterases showing preference for Trp. In this study, we investigated the role of Tyr(182) in the active site wall of hyperthermophilic esterase EstE1. Mutation of Tyr to Phe or Ala had a moderate effect on EstE1 thermal stability. However, a small-to-large mutation such as Tyr to His or Trp had a devastating effect on thermal stability. All mutant EstE1 enzymes showed reduced catalytic rates and enhanced substrate affinities as compared with wild-type EstE1. Hydrogen bond formation involving Tyr(182) was unimportant for maintaining EstE1 thermal stability, as the EstE1 structure is already adapted to high temperatures via increased intramolecular interactions. However, removal of hydrogen bond from Tyr(182) significantly decreased EstE1 catalytic activity, suggesting its role in stabilization of the active site. These results suggest that Tyr is preferred over a similarly sized Phe residue or bulky His or Trp residue in the active site walls of hyperthermophilic esterases for stabilizing the active site and regulating catalytic activity at high temperatures.

Polycyclic aromatic hydrocarbon degradation by biosurfactant-producing Pseudomonas sp. IR1.

PubMed

Kumara, Manoj; Leon, Vladimir; De Sisto Materano, Angela; Ilzins, Olaf A; Galindo-Castro, Ivan; Fuenmayor, Sergio L

2006-01-01

We characterized a newly isolated bacterium, designated as IR1, with respect to its ability to degrade polycyclic aromatic hydrocarbons (PAHs) and to produce biosurfactants. Isolated IR1 was identified as Pseudomonas putida by analysis of 16S rRNA sequences (99.6% homology). It was capable of utilizing two-, three- and four-ring PAHs but not hexadecane and octadecane as a sole carbon and energy source. PCR and DNA hybridization studies showed that enzymes involved in PAH metabolism were related to the naphthalene dioxygenase pathway. Observation of both tensio-active and emulsifying activities indicated that biosurfactants were produced by IR1 during growth on both water miscible and immiscible substrates. The biosurfactants lowered the surface tension of medium from 54.9 dN cm(-1) to 35.4 dN cm(-1) and formed a stable and compact emulsion with an emulsifying activity of 74% with diesel oil, when grown on dextrose. These findings indicate that this isolate may be useful for bioremediation of sites contaminated with aromatic hydrocarbons.

Probing the active site tryptophan of Staphylococcus aureus thioredoxin with an analog

PubMed Central

Englert, Markus; Nakamura, Akiyoshi; Wang, Yane-Shih; Eiler, Daniel; Söll, Dieter; Guo, Li-Tao

2015-01-01

Genetically encoded non-canonical amino acids are powerful tools of protein research and engineering; in particular they allow substitution of individual chemical groups or atoms in a protein of interest. One such amino acid is the tryptophan (Trp) analog 3-benzothienyl-l-alanine (Bta) with an imino-to-sulfur substitution in the five-membered ring. Unlike Trp, Bta is not capable of forming a hydrogen bond, but preserves other properties of a Trp residue. Here we present a pyrrolysyl-tRNA synthetase-derived, engineered enzyme BtaRS that enables efficient and site-specific Bta incorporation into proteins of interest in vivo. Furthermore, we report a 2.1 Å-resolution crystal structure of a BtaRS•Bta complex to show how BtaRS discriminates Bta from canonical amino acids, including Trp. To show utility in protein mutagenesis, we used BtaRS to introduce Bta to replace the Trp28 residue in the active site of Staphylococcus aureus thioredoxin. This experiment showed that not the hydrogen bond between residues Trp28 and Asp58, but the bulky aromatic side chain of Trp28 is important for active site maintenance. Collectively, our study provides a new and robust tool for checking the function of Trp in proteins. PMID:26582921

Identification of acidic and aromatic residues in the Zta activation domain essential for Epstein-Barr virus reactivation.

PubMed

Deng, Z; Chen, C J; Zerby, D; Delecluse, H J; Lieberman, P M

2001-11-01

Epstein-Barr virus (EBV) lytic cycle transcription and DNA replication require the transcriptional activation function of the viral immediate-early protein Zta. We describe a series of alanine substitution mutations in the Zta activation domain that reveal two functional motifs based on amino acid composition. Alanine substitution of single or paired hydrophobic aromatic amino acid residues resulted in modest transcription activation defects, while combining four substitutions of aromatic residues (F22/F26/W74/F75) led to more severe transcription defects. Substitution of acidic amino acid residue E27, D35, or E54 caused severe transcription defects on most viral promoters. Promoter- and cell-specific defects were observed for some substitution mutants. Aromatic residues were required for Zta interaction with TFIIA-TFIID and the CREB-binding protein (CBP) and for stimulation of CBP histone acetyltransferase activity in vitro. In contrast, acidic amino acid substitution mutants interacted with TFIIA-TFIID and CBP indistinguishably from the wild type. The nuclear domain 10 (ND10) protein SP100 was dispersed by most Zta mutants, but acidic residue mutations led to reduced, while aromatic substitution mutants led to increased SP100 nuclear staining. Acidic residue substitution mutants had more pronounced defects in transcription activation of endogenous viral genes in latently infected cells and for viral replication, as measured by the production of infectious virus. One mutant, K12/F13, was incapable of stimulating EBV lytic replication but had only modest transcription defects. These results indicate that Zta stimulates viral reactivation through two nonredundant structural motifs, one of which interacts with general transcription factors and coactivators, and the other has an essential but as yet not understood function in lytic transcription.

Metal-organic framework based in-syringe solid-phase extraction for the on-site sampling of polycyclic aromatic hydrocarbons from environmental water samples.

PubMed

Zhang, Xiaoqiong; Wang, Peiyi; Han, Qiang; Li, Hengzhen; Wang, Tong; Ding, Mingyu

2018-04-01

In-syringe solid-phase extraction is a promising sample pretreatment method for the on-site sampling of water samples because of its outstanding advantages of portability, simple operation, short extraction time, and low cost. In this work, a novel in-syringe solid-phase extraction device using metal-organic frameworks as the adsorbent was fabricated for the on-site sampling of polycyclic aromatic hydrocarbons from environmental waters. Trace polycyclic aromatic hydrocarbons were effectively extracted through the self-made device followed by gas chromatography with mass spectrometry analysis. Owing to the excellent adsorption performance of metal-organic frameworks, the analytes could be completely adsorbed during one adsorption cycle, thus effectively shortening the extraction time. Moreover, the adsorbed analytes could remain stable on the device for at least 7 days, revealing the potential of the self-made device for on-site sampling of degradable compounds in remote regions. The limit of detection ranged from 0.20 to 1.9 ng/L under the optimum conditions. Satisfactory recoveries varying from 84.4 to 104.5% and relative standard deviations below 9.7% were obtained in real samples analysis. The results of this study promote the application of metal-organic frameworks in sample preparation and demonstrate the great potential of in-syringe solid-phase extraction for the on-site sampling of trace contaminants in environmental waters. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Activity of selected aromatic amino acids in biological systems.

PubMed

Krzyściak, Wirginia

2011-01-01

Besides the structural function in proteins, aromatic amino acids are precursors of many important biological compounds essential for normal functioning of the human organism. Many of these compounds may be used as markers for identification of specific pathological states. Comprehensive knowledge about the metabolism of aromatic amino acids and mechanisms of action of their metabolites made it possible to develop effective treatments for many disorders. However, it should not be forgotten that in some pathological conditions, these compounds could not only be involved in the pathogenesis of many disease entities but could also be used as an important tool in prediction of many diseases. This paper contains a review of published literature on aromatic amino acids in the context of physiological processes of the human body and chosen social disorders, such as cancers; psychiatric disorders: depression, anxiety states, schizophrenia, bipolar affective disorders; neurodegenerative, and cardiovascular diseases; chronic kidney insufficiency or diabetes.

Aromatic hydrocarbons at urban, sub-urban, rural (8°52'N; 67°19'W) and remote sites in Venezuela

NASA Astrophysics Data System (ADS)

Holzinger, R.; Kleiss, B.; Donoso, L.; Sanhueza, E.

Using the novel on-line proton transfer reaction mass spectrometry (PTR-MS) technique, atmospheric concentrations of benzene, toluene, xylenes, and C 9-benzenes were measured in Caracas (urban), Altos de Pipe (sub-urban), Calabozo (rural) and Parupa (remote), during various campaigns in 1999 and 2000. Average daytime mixing ratios measured in Caracas are 1.1, 3.2, 3.7, and 2.7 nmol/mol for benzene, toluene, xylenes, and C 9-benzenes. At the sub-urban site, located only few km from Caracas, relatively low levels (˜20% of the levels measured in Caracas) of these aromatic hydrocarbons were observed. At the rural site during the dry season, higher concentrations of benzene (0.15 nmol/mol) were recorded, whereas those of toluene (0.08 nmol/mol) were lower during that time. The aromatic hydrocarbon ratios in the wet season (benzene: 0.08 nmol/mol; toluene: 0.09 nmol/mol) are consistent with an aged urban plume, whereas biomass burning emissions dominate during the dry season. From rural and urban [benzene]/[toluene] ratios a mean HO concentration of 2.6×10 6 molecules/cm 3 was estimated during the wet season. This value must be considered an overestimate because it does not account for background concentrations which are likely for benzene and toluene. At the remote "La Gran Sabana" region (Parupa) very low mixing ratios (0.031 and 0.015 nmol/mol for benzene and toluene) are showing the pristine region to be unaffected by local sources. From the [benzene]/[toluene] ratio we deduced, that "urban" air arriving from the coastline (350 km) is likely mixed with air containing some background of benzene and toluene. Urban emissions (automobiles) should be the major source of aromatic compounds, however, during the dry season biomass burning seems to make an important contribution.

Structural insight into the active site of mushroom tyrosinase using phenylbenzoic acid derivatives.

PubMed

Oyama, Takahiro; Yoshimori, Atsushi; Takahashi, Satoshi; Yamamoto, Tetsuya; Sato, Akira; Kamiya, Takanori; Abe, Hideaki; Abe, Takehiko; Tanuma, Sei-Ichi

2017-07-01

So far, many inhibitors of tyrosinase have been discovered for cosmetic and clinical agents. However, the molecular mechanisms underlying the inhibition in the active site of tyrosinase have not been well understood. To explore this problem, we examined here the inhibitory effects of 4'-hydroxylation and methoxylation of phenylbenzoic acid (PBA) isomers, which have a unique scaffold to inhibit mushroom tyrosinase. The inhibitory effect of 3-PBA, which has the most potent inhibitory activity among the isomers, was slightly decreased by 4'-hydroxylation and further decreased by 4'-methoxylation against mushroom tyrosinase. Surprisingly, 4'-hydroxylation but not methoxylation of 2-PBA appeared inhibitory activity. On the other hand, both 4'-hydroxylation and methoxylation of 4-PBA increased the inhibitory activity against mushroom tyrosinase. In silico docking analyses using the crystallographic structure of mushroom tyrosinase indicated that the carboxylic acid or 4'-hydroxyl group of PBA derivatives could chelate with cupric ions in the active site of mushroom tyrosinase, and that the interactions of Asn260 and Phe264 in the active site with the adequate-angled biphenyl group are involved in the inhibitory activities of the modified PBAs, by parallel and T-shaped π-π interactions, respectively. Furthermore, Arg268 could fix the angle of the aromatic ring of Phe264, and Val248 is supposed to interact with the inhibitors as a hydrophobic manner. These results may enhance the structural insight into mushroom tyrosinase for the creation of novel tyrosinase inhibitors. Copyright © 2017 Elsevier Ltd. All rights reserved.

Destruction and survival of polycyclic aromatic hydrocarbons in active galaxies

NASA Technical Reports Server (NTRS)

Voit, G. M.

1992-01-01

Infrared spectra of dusty galactic environments often contain emission features attributed to polycyclic aromatic hydrocarbons or PAHs, which can be considered to be very small grains or very large molecules. Although IR spectra of starburst galaxies almost always show these emission features, similar spectra of active galaxies are usually featureless. Even in those active galaxies that do exhibit PAH emission, the PAHs still appear to be eradicated from the nuclear region. This dichotomy suggests that PAHs are destroyed by the intense hard radiation field from an AGN. Laboratory experiments show that certain PAHs are, in fact, so effectively destroyed by individual EUV and X-ray photons that they cannot survive even at kiloparsec distances from active nuclei. Regions within active galaxies that do show PAH emission must therefore be shielded from the central X-ray source by a substantial column density of X-ray absorbing gas.

Human 15-LOX-1 active site mutations alter inhibitor binding and decrease potency.

PubMed

Armstrong, Michelle; van Hoorebeke, Christopher; Horn, Thomas; Deschamps, Joshua; Freedman, J Cody; Kalyanaraman, Chakrapani; Jacobson, Matthew P; Holman, Theodore

2016-11-01

Human 15-lipoxygenase-1 (h15-LOX-1 or h12/15-LOX) reacts with polyunsaturated fatty acids and produces bioactive lipid derivatives that are implicated in many important human diseases. One such disease is stroke, which is the fifth leading cause of death and the first leading cause of disability in America. The discovery of h15-LOX-1 inhibitors could potentially lead to novel therapeutics in the treatment of stroke, however, little is known about the inhibitor/active site interaction. This study utilizes site-directed mutagenesis, guided in part by molecular modeling, to gain a better structural understanding of inhibitor interactions within the active site. We have generated eight mutants (R402L, R404L, F414I, F414W, E356Q, Q547L, L407A, I417A) of h15-LOX-1 to determine whether these active site residues interact with two h15-LOX-1 inhibitors, ML351 and an ML094 derivative, compound 18. IC 50 values and steady-state inhibition kinetics were determined for the eight mutants, with four of the mutants affecting inhibitor potency relative to wild type h15-LOX-1 (F414I, F414W, E356Q and L407A). The data indicate that ML351 and compound 18, bind in a similar manner in the active site to an aromatic pocket close to F414 but have subtle differences in their specific binding modes. This information establishes the binding mode for ML094 and ML351 and will be leveraged to develop next-generation inhibitors. Copyright © 2016 Elsevier Ltd. All rights reserved.

Spatial distribution of polycyclic aromatic hydrocarbons in soil, sediment, and combusted residue at an e-waste processing site in southeast China.

PubMed

Leung, Anna O W; Cheung, Kwai Chung; Wong, Ming Hung

2015-06-01

The environmental pollution and health impacts caused by the primitive and crude recycling of e-waste have become urgent global issues. Guiyu, China is a major hotspot of e-waste recycling. In this study, the levels and distribution of polycyclic aromatic hydrocarbons in soil in Guiyu were determined to investigate the effect of e-waste activities on the environment and to identify possible sources of these pollutants. Sediment samples from a local duck pond, water gullies, a river tributary, and combusted residue from e-waste burning sites were also investigated. The general trend found in soil (Σ16 PAHs) was acid leaching site > duck pond > rice field > printer roller dump site > reservoir (control site) and ranged from 95.2 ± 54.2 to 5,210 ± 89.6 ng/g (dry wt). The highest average total PAH concentrations were found in combusted residues of wires, cables, and other computer electrical components located at two e-waste open burning sites (18,600 and 10,800 ± 3,940 ng/g). These were 195- and 113-fold higher than the PAH concentrations of soil at the control site. Sediment PAH concentrations ranged from 37.2 ± 6 to 534 ± 271 ng/g. Results of this study provide further evidence of significant input of PAHs to the environment attributed to crude e-waste recycling.

Nucleophilic Aromatic Substitution.

ERIC Educational Resources Information Center

Avila, Walter B.; And Others

1990-01-01

Described is a microscale organic chemistry experiment which demonstrates one feasible route in preparing ortho-substituted benzoic acids and provides an example of nucleophilic aromatic substitution chemistry. Experimental procedures and instructor notes for this activity are provided. (CW)

Atmospheric behaviors of particulate-bound polycyclic aromatic hydrocarbons and nitropolycyclic aromatic hydrocarbons in Beijing, China from 2004 to 2010

NASA Astrophysics Data System (ADS)

Tang, Ning; Suzuki, Genki; Morisaki, Hiroshi; Tokuda, Takahiro; Yang, Xiaoyang; Zhao, Lixia; Lin, Jinming; Kameda, Takayuki; Toriba, Akira; Hayakawa, Kazuichi

2017-03-01

Airborne particulates were collected at an urban site (site 1) from 2004 to 2010 and at a suburban site (site 2) in 2010 in Beijing. Nine polycyclic aromatic hydrocarbons (PAHs) and five nitropolycyclic aromatic hydrocarbons (NPAHs) in the airborne particulates were determined by HPLC with fluorescence and chemiluminescence detection, respectively. The concentrations of PAHs and NPAHs were higher in heating season than in non-heating season at the two sites. Both the concentrations of PAHs and NPAHs decreased in the non-heating season but only the concentrations of NPAHs decreased in heating season at site 1, from 2004 to 2010. These findings suggest that source control measures implemented by the city of Beijing helped to reduce air pollution in Beijing. The concentrations of PAHs increased at site 1 in 2010, possibly because of the transport of emissions from windward other areas, such as Shanxi province. Several diagnostic ratios of PAHs and NPAHs showed that the different sources contributed to Beijing's air pollution, although coal combustion was the main source in the heating season and vehicle emission was the main source in the non-heating season. An analysis of physical parameters at Beijing showed that high wind speed can remove atmospheric PAHs and NPAHs in the heating season and that high relative humidity can remove them in the non-heating season.

Polyphenylquinoxalines via aromatic nucleophilic displacement

NASA Technical Reports Server (NTRS)

Hergenrother, Paul M. (Inventor); Connell, John W. (Inventor)

1990-01-01

Polyphenylquinoxalines are prepared by the nucleophilic displacement reaction of di(hydroxyphenyl)quinoxaline monomers with activated aromatic dihalides or dinitro compounds. The reactions are carried out in polar aprotic solvents using alkali metal bases at elevated temperatures under nitrogen. The di(hydroxyphenyl)quinoxaline monomers are prepared either by reacting stoichiometric quantities of aromatic bis(o-diamines) with a hydroxybenzil or by reacting o-phenylenediamine with a dihydroxybenzil or bis(hydroxyphenylglyoxylyl)benzene.

Polyphenylquinoxalines via aromatic nucleophilic displacement

NASA Technical Reports Server (NTRS)

Hergenrother, Paul M. (Inventor); Connell, John W. (Inventor)

1991-01-01

Polyphenylquinoxalines are prepared by the nucleophilic displacement reaction of di(hydroxyphenyl)quinoxaline monomers with activated aromatic dihalides or dinitro compounds. The reactions are carried out in polar aprotic solvents during alkali metal bases at elevated temperatures under nitrogen. The di(hydroxyphenyl)quinoxaline monomers are prepared either by reacting stoichiometric quantities of aromatic bis(o-diamines) with a hydroxybenzil or by reacting o-phenylenediamine with a dihydroxybenzil or bis(hydroxyphenylglyoxylyl)benzene.

Lignans and aromatic glycosides from Piper wallichii and their antithrombotic activities.

PubMed

Shi, Yan-Ni; Shi, Yi-Ming; Yang, Lian; Li, Xing-Cong; Zhao, Jin-Hua; Qu, Yan; Zhu, Hong-Tao; Wang, Dong; Cheng, Rong-Rong; Yang, Chong-Ren; Xu, Min; Zhang, Ying-Jun

2015-03-13

Piper wallichii (Miq.) Hand.-Mazz. is a medicinal plant used widely for the treatment of rheumatoid arthritis, inflammatory diseases, cerebral infarction and angina in China. Previous study showed that lignans and neolignans from Piper spp. had potential inhibitory activities on platelet aggregation. In the present study, we investigated the chemical constituents of Piper wallichii and their antithrombotic activities, to support its traditional uses. The methanolic extract of the air-dried stems of Piper wallichii was separated and purified using various chromatographic methods, including semi-preparative HPLC. The chemical structures of the isolates were determined by detailed spectroscopic analysis, and acidic hydrolysis in case of the new glycoside 2. Determination of absolute configurations of the new compound 1 was facilitated by calculated electronic circular dichroism using time-dependent density-functional theory. All compounds were tested for their inhibitory effects on platelet aggregation induced by platelet activating factor (PAF) in rabbits׳ blood model, from which the active ones were further evaluated the in vivo antithrombotic activity in zebrafish model. A new neolignan, piperwalliol A (1), and four new aromatic glycosides, piperwalliosides A-D (2-5) were isolated from the stems of Piper wallichii, along with 25 known compounds, including 13 lignans, six aromatic glycosides, two phenylpropyl aldehydes, and four biphenyls. Five known compounds (6-10) showed in vitro antiplatelet aggregation activities. Among them, (-)-syringaresinol (6) was the most active compound with an IC50 value of 0.52 mM. It is noted that in zebrafish model, the known lignan 6 showed good in vivo antithrombotic effect with a value of 37% at a concentration of 30 μM, compared with the positive control aspirin with the inhibitory value of 74% at a concentration of 125μM. This study demonstrated that lignans, phenylpropanoid and biphenyl found in Piper wallichii may be

Heterocyclic aromatic hydrocarbons show estrogenic activity upon metabolization in a recombinant transactivation assay.

PubMed

Brinkmann, Markus; Maletz, Sibylle; Krauss, Martin; Bluhm, Kerstin; Schiwy, Sabrina; Kuckelkorn, Jochen; Tiehm, Andreas; Brack, Werner; Hollert, Henner

2014-05-20

Heterocyclic aromatic hydrocarbons (hetero-PAHs) are increasingly studied at contaminated sites; especially at former industrial facilities where coal tar-oil was handled, e.g., wood treatment plants, high concentrations of hetero-PAHs are frequently detected in groundwater plumes. In previous studies, fractions of groundwater with high estrogenic activity contained hetero-PAHs and their hydroxylated metabolites. To evaluate this preliminary evidence, selected hetero-PAHs were screened for their estrogenic activity in lyticase yeast estrogen screen (LYES) and ER CALUX. All tested substances were inactive in the LYES. Hetero-PAHs such as acridine, xanthene, indole, 2-methylbenzofuran, 2,3-dimethylbenzofuran, dibenzofuran, dibenzothiophene, quinoline, and 6-methylquinoline were positive in the ER CALUX, with estradiol equivalence factors (EEFs) from 2.85 × 10(-7) to 3.18 × 10(-5). The EEF values of these substances were comparable to those of other xenoestrogens (e.g., alkylphenols or bisphenol A) that are sometimes found in surface water. Chemical analyses revealed that T47Dluc cells could metabolize most of the substances. Among the metabolites (tentatively) identified by liquid chromatography-tandem mass spectrometry (LC-MS/MS) were hydroxides and their keto tautomers, sulfates, sulfoxides, and N-oxides. Because of their high concentrations measured in groundwater, we conclude that hetero-PAHs and metabolites may be a potential risk and should be the subject of further research.

Aromatic C=C bonds as dipolarophiles: facile reactions of uncomplexed electron-deficient benzene derivatives and other aromatic rings with a non-stabilized azomethine ylide.

PubMed

Lee, Sunyoung; Diab, Sonia; Queval, Pierre; Sebban, Muriel; Chataigner, Isabelle; Piettre, Serge R

2013-05-27

Non-stabilized azomethine ylide 4a reacts smoothly at room temperature with a variety of uncomplexed aromatic heterocycles and carbocycles on the condition that the ring contains at least one or two electron-withdrawing substituents, respectively. Aromatic substrates, including pyridine and benzene derivatives, participate as 2π components in [3+2] cycloaddition reactions and interact with one, two, or three equivalent(s) of the ylide, depending on their structure and substitution pattern. Thus, this process affords highly functionalized polycyclic structures that contain between one and three pyrrolidinyl ring(s) in useful yields. These results indicate that the site selectivity of the cycloaddition reactions strongly depends on both the nature and the positions of the substituents. In most cases, the second 1,3-dipolar reaction occurs on the opposite face to the one that contains the first pyrrolidinyl ring. DFT calculations on model compounds indicate that a concerted mechanism features a low activation barrier. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Antimicrobial activity of essential oils from Mediterranean aromatic plants against several foodborne and spoilage bacteria.

PubMed

Silva, Nuno; Alves, Sofia; Gonçalves, Alexandre; Amaral, Joana S; Poeta, Patrícia

2013-12-01

The antimicrobial activity of essential oils extracted from a variety of aromatic plants, often used in the Portuguese gastronomy was studied in vitro by the agar diffusion method. The essential oils of thyme, oregano, rosemary, verbena, basil, peppermint, pennyroyal and mint were tested against Gram-positive (Listeria monocytogenes, Clostridium perfringens, Bacillus cereus, Staphylococcus aureus, Enterococcus faecium, Enterococcus faecalis, and Staphylococcus epidermidis) and Gram-negative strains (Salmonella enterica, Escherichia coli, and Pseudomonas aeruginosa). For most essential oils examined, S. aureus, was the most susceptible bacteria, while P. aeruginosa showed, in general, least susceptibility. Among the eight essential oils evaluated, thyme, oregano and pennyroyal oils showed the greatest antimicrobial activity, followed by rosemary, peppermint and verbena, while basil and mint showed the weakest antimicrobial activity. Most of the essential oils considered in this study exhibited a significant inhibitory effect. Thyme oil showed a promising inhibitory activity even at low concentration, thus revealing its potential as a natural preservative in food products against several causal agents of foodborne diseases and food spoilage. In general, the results demonstrate that, besides flavoring the food, the use of aromatic herbs in gastronomy can also contribute to a bacteriostatic effect against pathogens.

PHOTOACTIVATED TOXICITY IN AMPHIPODS COLLECTED FROM POLYCYCLIC AROMATIC HYDROCARBON-CONTAMINATED SITES

EPA Science Inventory

The risk of photo-activated PAH toxicity in contaminated aquatic systems has not been well characterized. To better indicate this potential, amphipods (Gammarus spp.) were collected from two PAH contaminated sites (Hog Island and USX), as well as a reference site (Chipmunk Cove)...

Synthesis and antimicrobial activity of novel amphiphilic aromatic amino alcohols.

PubMed

de Almeida, Angelina M; Nascimento, Thiago; Ferreira, Bianca S; de Castro, Pedro P; Silva, Vânia L; Diniz, Claúdio G; Le Hyaric, Mireille

2013-05-15

We report in this work the preparation and in vitro antimicrobial evaluation of novel amphiphilic aromatic amino alcohols synthesized by reductive amination of 4-alkyloxybenzaldehyde with 2-amino-2-hydroxymethyl-propane-1,3-diol. The antibacterial activity was determined against four standard strains (Staphylococcus aureus, Staphylococcus epidermidis, Escherichia coli, Pseudomonas aeruginosa) and 21 clinical isolates of methicillin-resistant Staphylococcus aureus. The antifungal activity was evaluated against four yeast (Candida albicans, Candida tropicalis, Candida glabrata and Candida parapsilosis). The results obtained showed a strong positive correlation between the lipophilicity and the antibiotic activity of the tested compounds. The best activities were obtained against the Gram-positive bacteria (MIC=2-16μgml(-1)) for the five compounds bearing longer alkyl chains (4c-g; 8-14 carbons), which were also the most active against Candida (MIC=2-64μgml(-1)). Compound 4e exhibited the highest levels of inhibitory activity (MIC=2-16μgml(-1)) against clinical isolates of MRSA. A concentration of twice the MIC resulted in bactericidal activity of 4d against 19 of the 21 clinical isolates. Copyright © 2013 Elsevier Ltd. All rights reserved.

SEDIMENT-ASSOCIATED REACTIONS OF AROMATIC AMINES: QSAR DEVELOPMENT

EPA Science Inventory

Despite the common occurrence of the aromatic amine functional group in environmental contaminants, few quantitative structure-activity relationships (QSARs) have been developed to predict sorption kinetics for aromatic amines in natural soils and sediments. Towards the goal of d...

On the inhibition of muscle membrane chloride conductance by aromatic carboxylic acids

PubMed Central

Palade, PT; Barchi, RL

1977-01-01

25 aromatic carboxylic acids which are analogs of benzoic acid were tested in the rat diaphragm preparation for effects on chloride conductance (G(Cl)). Of the 25, 19 were shown to reduce membrane G(Cl) with little effect on other membrane parameters, although their apparent K(i) varied widely. This inhibition was reversible if exposure times were not prolonged. The most effective analog studied was anthracene-9-COOH (9-AC; K(i) = 1.1 x 10(-5) M). Active analogs produced concentration-dependent inhibition of a type consistent with interaction at a single site or group of sites having similar binding affinities, although a correlation could also be shown between lipophilicity and K(i). Structure-activity analysis indicated that hydrophobic ring substitution usually increased inhibitory activity while para polar substitutions reduced effectiveness. These compounds do not appear to inhibit G(Cl) by altering membrane surface charge and the inhibition produced is not voltage dependent. Qualitative characteristics of the I-V relationship for Cl(-) current are not altered. Conductance to all anions is not uniformly altered by these acids as would be expected from steric occlusion of a common channel. Concentrations of 9-AC reducing G(Cl) by more than 90 percent resulted in slight augmentation of G(I). The complete conductance sequence obtained at high levels of 9-AC was the reverse of that obtained under control conditions. Permeability sequences underwent progressive changes with increasing 9-AC concentration and ultimately inverted at high levels of the analog. Aromatic carboxylic acids appear to inhibit G(Cl) by binding to a specific intramembrane site and altering the selectivity sequence of the membrane anion channel. PMID:894246

Poly(N-arylenbenzimidazoles) via aromatic nucleophilic displacement

NASA Technical Reports Server (NTRS)

Connell, John W. (Inventor); Hergenrother, Paul M. (Inventor); Smith, Joseph G., Jr. (Inventor)

1995-01-01

Novel poly(N-arylenebenzimidazole)s (PNABIs) are prepared by the aromatic nucleophilic displacement reaction of novel di(hydroxyphenyl-N-arylene benzimidazole) monomers with activated aromatic dihalides or activated aromatic dinitro compounds. The polymerizations are carried out in polar aprotic solvents such as N-methyl-2-pyrrolidinone or N,N-dimethylacetamide using alkali metal bases such as potassium carbonate at elevated temperatures under nitrogen. The di(hydroxyphenyl N-arylenebenzimidazole) monomers are synthesized by reacting phenyl 4-hydroxybenzoate with bis(2-aminoanilino) arylenes in diphenylsulfone. Moderate molecular weight PNABIs of new chemical structures were prepared that exhibit a favorable combination of physical and mechanical properties. The use of the novel di(hydroxyphenyl N-arylenebenzimidazole)s permits a more economical and easier way to prepare PNABIs than previous routes.

Aromatic as well as aliphatic hydrocarbon solvent axonopathy.

PubMed

Spencer, Peter S; Kim, Min Sun; Sabri, Mohammad I

2002-03-01

Superfund sites that contain mixtures of aromatic and aliphatic solvents represent an undefined health hazard. After prolonged exposure to relatively high levels of certain aliphatic solvents (e.g. n-hexane, 2-hexanone), humans and animals develop a dose-dependent neurodegeneration that occurs clinically as a symmetrical peripheral neuropathy. This is triggered by the action of 2,5-hexanedione (1,2-diacetylethane), a 1,4-diketone (gamma-diketone) metabolite that targets proteins required for the maintenance of neuronal (and testicular Sertoli cell) integrity. Certain aromatic solvents (1,2-diethylbenzene, 1,2,4-triethylbenzene) cause electrophysiological changes consistent with sensorimotor neuropathy in rodents, but the underlying mechanisms and pathogenesis are unclear. Our recent studies show that the o-diacetyl derivative and likely metabolite of 1,2-diethylbenzene, 1,2-diacetylbenzene, behaves as a neurotoxic (aromatic) gamma-diketone of high neurotoxic potency. Rats treated with 1,2-diacetylbenzene develop limb weakness associated with proximal, neurofilament-filled giant axonal swellings comparable to those seen in animals treated with the potent 3,4-dimethyl derivative of 2,5-hexanedione. The blue chromogen induced by treatment with 1,2-diacetylbenzene is under study as a possible urinary biomarker of exposure to aromatic solvents (e.g. 1,2-diethylbenzene, tetralin) with neurotoxic potential. Development and validation of sensitive new biomarkers, especially for non-cancer endpoints, will aid in assessing the health risk associated with exposure to hazardous substances at Superfund sites.

Enhancing muconic acid production from glucose and lignin-derived aromatic compounds via increased protocatechuate decarboxylase activity

DOE PAGES

Johnson, Christopher W.; Salvachua, Davinia; Khanna, Payal; ...

2016-04-22

The conversion of biomass-derived sugars and aromatic molecules to cis,cis-muconic acid (referred to hereafter as muconic acid or muconate) has been of recent interest owing to its facile conversion to adipic acid, an important commodity chemical. Metabolic routes to produce muconate from both sugars and many lignin-derived aromatic compounds require the use of a decarboxylase to convert protocatechuate (PCA, 3,4-dihydroxybenzoate) to catechol (1,2-dihydroxybenzene), two central aromatic intermediates in this pathway. Several studies have identified the PCA decarboxylase as a metabolic bottleneck, causing an accumulation of PCA that subsequently reduces muconate production. A recent study showed that activity of the PCAmore » decarboxylase is enhanced by co-expression of two genetically associated proteins, one of which likely produces a flavin-derived cofactor utilized by the decarboxylase. Using entirely genome-integrated gene expression, we have engineered Pseudomonas putida KT2440-derived strains to produce muconate from either aromatic molecules or sugars and demonstrate in both cases that co-expression of these decarboxylase associated proteins reduces PCA accumulation and enhances muconate production relative to strains expressing the PCA decarboxylase alone. In bioreactor experiments, co-expression increased the specific productivity (mg/g cells/h) of muconate from the aromatic lignin monomer p-coumarate by 50% and resulted in a titer of >15 g/L. In strains engineered to produce muconate from glucose, co-expression more than tripled the titer, yield, productivity, and specific productivity, with the best strain producing 4.92+/-0.48 g/L muconate. Furthermore, this study demonstrates that overcoming the PCA decarboxylase bottleneck can increase muconate yields from biomass-derived sugars and aromatic molecules in industrially relevant strains and cultivation conditions.« less

Adsorption of aromatic compounds by carbonaceous adsorbents: a comparative study on granular activated carbon, activated carbon fiber, and carbon nanotubes.

PubMed

Zhang, Shujuan; Shao, Ting; Kose, H Selcen; Karanfil, Tanju

2010-08-15

Adsorption of three aromatic organic compounds (AOCs) by four types of carbonaceous adsorbents [a granular activated carbon (HD4000), an activated carbon fiber (ACF10), two single-walled carbon nanotubes (SWNT, SWNT-HT), and a multiwalled carbon nanotube (MWNT)] with different structural characteristics but similar surface polarities was examined in aqueous solutions. Isotherm results demonstrated the importance of molecular sieving and micropore effects in the adsorption of AOCs by carbonaceous porous adsorbents. In the absence of the molecular sieving effect, a linear relationship was found between the adsorption capacities of AOCs and the surface areas of adsorbents, independent of the type of adsorbent. On the other hand, the pore volume occupancies of the adsorbents followed the order of ACF10 > HD4000 > SWNT > MWNT, indicating that the availability of adsorption site was related to the pore size distributions of the adsorbents. ACF10 and HD4000 with higher microporous volumes exhibited higher adsorption affinities to low molecular weight AOCs than SWNT and MWNT with higher mesopore and macropore volumes. Due to their larger pore sizes, SWNTs and MWNTs are expected to be more efficient in adsorption of large size molecules. Removal of surface oxygen-containing functional groups from the SWNT enhanced adsorption of AOCs.

Characterisation and risk assessment of polycyclic aromatic hydrocarbons (PAHs) in soils and plants around e-waste dismantling sites in southern China.

PubMed

Wang, Yujie; He, Jiexin; Wang, Shaorui; Luo, Chunling; Yin, Hua; Zhang, Gan

2017-10-01

Environmental pollution due to primitive e-waste dismantling activities has been intensively investigated over the last decade in the south-eastern coastal region of China. In the present study, we investigated the distribution and composition of polycyclic aromatic hydrocarbons (PAHs) in soils and plants around e-waste recycling sites in Longtang, Guangdong province, South China. The results indicated that PAH concentrations in rhizosphere soil and non-rhizosphere soil were in the range of 133 to 626 ng/g and 60 to 816 ng/g, respectively, while PAH levels in plant tissue were 96 to 388 ng/g in shoots and 143 to 605 ng/g in roots. PAHs were enriched in rhizosphere soils in comparison with non-rhizosphere soils. The concentrations of PAHs in plant tissues varied greatly among plant cultivars, indicating that the uptake of PAHs by plants is species-dependent. Different profiles of PAHs in the soil and the corresponding plant tissue implied that PAH uptake and translocation by plants were selective.The total daily intakes of PAHs and carcinogenic PAHs through vegetables at the e-waste recycling site were estimated to be 99 and 22 ng/kg/day, respectively, suggesting that potential health risks associated with the consumption of contaminated vegetables should not be ignored.

Experimental and computational investigation of acetic acid deoxygenation over oxophilic molybdenum carbide: Surface chemistry and active site identity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schaidle, Joshua A.; Blackburn, Jeffrey; Farberow, Carrie A.

Ex situ catalytic fast pyrolysis (CFP) is a promising route for producing fungible biofuels; however, this process requires bifunctional catalysts that favor C–O bond cleavage, activate hydrogen at near atmospheric pressure and high temperature (350–500 °C), and are stable under high-steam, low hydrogen-to-carbon environments. Recently, early transition-metal carbides have been reported to selectively cleave C–O bonds of alcohols, aldehydes, and oxygenated aromatics, yet there is limited understanding of the metal carbide surface chemistry under reaction conditions and the identity of the active sites for deoxygenation. In this study, we evaluated molybdenum carbide (Mo 2C) for the deoxygenation of acetic acid,more » an abundant component of biomass pyrolysis vapors, under ex situ CFP conditions, and we probed the Mo 2C surface chemistry, identity of the active sites, and deoxygenation pathways using in situ diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS), X-ray photoelectron spectroscopy (XPS), and density functional theory (DFT) calculations.« less

Experimental and computational investigation of acetic acid deoxygenation over oxophilic molybdenum carbide: Surface chemistry and active site identity

DOE PAGES

Schaidle, Joshua A.; Blackburn, Jeffrey; Farberow, Carrie A.; ...

2016-01-21

Ex situ catalytic fast pyrolysis (CFP) is a promising route for producing fungible biofuels; however, this process requires bifunctional catalysts that favor C–O bond cleavage, activate hydrogen at near atmospheric pressure and high temperature (350–500 °C), and are stable under high-steam, low hydrogen-to-carbon environments. Recently, early transition-metal carbides have been reported to selectively cleave C–O bonds of alcohols, aldehydes, and oxygenated aromatics, yet there is limited understanding of the metal carbide surface chemistry under reaction conditions and the identity of the active sites for deoxygenation. In this study, we evaluated molybdenum carbide (Mo 2C) for the deoxygenation of acetic acid,more » an abundant component of biomass pyrolysis vapors, under ex situ CFP conditions, and we probed the Mo 2C surface chemistry, identity of the active sites, and deoxygenation pathways using in situ diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS), X-ray photoelectron spectroscopy (XPS), and density functional theory (DFT) calculations.« less

Factors That Affect Oxygen Activation and Coupling of the Two Redox Cycles in the Aromatization Reaction Catalyzed by NikD, an Unusual Amino Acid Oxidase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kommoju, Phaneeswara-Rao; Bruckner, Robert C.; Ferreira, Patricia

2009-10-21

NikD is a flavoprotein oxidase that catalyzes the oxidation of piperideine-2-carboxylate (P2C) to picolinate in a remarkable aromatization reaction comprising two redox cycles and at least one isomerization step. Tyr258 forms part of an 'aromatic cage' that surrounds the ring in picolinate and its precursors. Mutation of Tyr258 to Phe does not perturb the structure of nikD but does affect the coupling of the two redox cycles and causes a 10-fold decrease in turnover rate. Tyr258Phe catalyzes a quantitative two-electron oxidation of P2C, but only 60% of the resulting dihydropicolinate intermediate undergoes a second redox cycle to produce picolinate. Themore » mutation does not affect product yield with an alternate substrate (3,4-dehydro-l-proline) that is aromatized in a single two-electron oxidation step. Wild-type and mutant enzymes exhibit identical rate constants for oxidation of P2C to dihydropicolinate and isomerization of a reduced enzyme-dihydropicolinate complex. The observed rates are 200- and 10-fold faster, respectively, than the mutant turnover rate. Release of picolinate from Tyr258Phe is 100-fold faster than turnover. The presence of a bound substrate or product is a key factor in oxygen activation by wild-type nikD, as judged by the 10-75-fold faster rates observed for complexes of the reduced enzyme with picolinate, benzoate, or 1-cyclohexenoate, a 1-deaza-P2C analogue. The reduced Tyr258Phe-1-cyclohexenoate complex is 25-fold less reactive with oxygen than the wild-type complex. We postulate that mutation of Tyr258 causes subtle changes in active site dynamics that promote release of the reactive dihydropicolinate intermediate and disrupt the efficient synchronization of oxygen activation observed with wild-type nikD.« less

Reprogramming the Chemodiversity of Terpenoid Cyclization by Remolding the Active Site Contour of epi-Isozizaene Synthase

PubMed Central

2015-01-01

The class I terpenoid cyclase epi-isozizaene synthase (EIZS) utilizes the universal achiral isoprenoid substrate, farnesyl diphosphate, to generate epi-isozizaene as the predominant sesquiterpene cyclization product and at least five minor sesquiterpene products, making EIZS an ideal platform for the exploration of fidelity and promiscuity in a terpenoid cyclization reaction. The hydrophobic active site contour of EIZS serves as a template that enforces a single substrate conformation, and chaperones subsequently formed carbocation intermediates through a well-defined mechanistic sequence. Here, we have used the crystal structure of EIZS as a guide to systematically remold the hydrophobic active site contour in a library of 26 site-specific mutants. Remolded cyclization templates reprogram the reaction cascade not only by reproportioning products generated by the wild-type enzyme but also by generating completely new products of diverse structure. Specifically, we have tripled the overall number of characterized products generated by EIZS. Moreover, we have converted EIZS into six different sesquiterpene synthases: F96A EIZS is an (E)-β-farnesene synthase, F96W EIZS is a zizaene synthase, F95H EIZS is a β-curcumene synthase, F95M EIZS is a β-acoradiene synthase, F198L EIZS is a β-cedrene synthase, and F96V EIZS and W203F EIZS are (Z)-γ-bisabolene synthases. Active site aromatic residues appear to be hot spots for reprogramming the cyclization cascade by manipulating the stability and conformation of critical carbocation intermediates. A majority of mutant enzymes exhibit only relatively modest 2–100-fold losses of catalytic activity, suggesting that residues responsible for triggering substrate ionization readily tolerate mutations deeper in the active site cavity. PMID:24517311

AGRONOMIC OPTIMIZATION FOR PHYTOREMEDIATION OF POLYCYCLIC AROMATIC HYDROCARBONS

EPA Science Inventory

Phytoremediation is a low-cost method of using plants to degrade, volatilize or sequester organic and metal pollutants that has been used in efforts to remediate sites contaminated with polycyclic aromatic hydrocarbon (PAH) refinery wastes. Non-native plant species aggressivel...

Site-selective arene C-H amination via photoredox catalysis.

PubMed

Romero, Nathan A; Margrey, Kaila A; Tay, Nicholas E; Nicewicz, David A

2015-09-18

Over the past several decades, organometallic cross-coupling chemistry has developed into one of the most reliable approaches to assemble complex aromatic compounds from preoxidized starting materials. More recently, transition metal-catalyzed carbon-hydrogen activation has circumvented the need for preoxidized starting materials, but this approach is limited by a lack of practical amination protocols. Here, we present a blueprint for aromatic carbon-hydrogen functionalization via photoredox catalysis and describe the utility of this strategy for arene amination. An organic photoredox-based catalyst system, consisting of an acridinium photooxidant and a nitroxyl radical, promotes site-selective amination of a variety of simple and complex aromatics with heteroaromatic azoles of interest in pharmaceutical research. We also describe the atom-economical use of ammonia to form anilines, without the need for prefunctionalization of the aromatic component. Copyright © 2015, American Association for the Advancement of Science.

Assessment of polycyclic aromatic hydrocarbons (PAHs) contamination in surface soil of coal stockpile sites in South Kalimantan, Indonesia.

PubMed

Mizwar, Andy; Priatmadi, Bambang Joko; Abdi, Chairul; Trihadiningrum, Yulinah

2016-03-01

Concentrations, spatial distribution, and sources of 16 polycyclic aromatic hydrocarbons (PAHs), listed as priority pollutants by the United States Environmental Protection Agency (USEPA), were investigated in surface soils of three different coal stockpile, agricultural, and residential sites in South Kalimantan Province, Indonesia. Total PAHs concentration ranged from 4.69 to 22.67 mg kg(-1)-dw. PAHs concentrations in soil of coal stockpile sites were higher than those in agricultural and residential soil. A complex of petrogenic origin and pyrolytic sources was found within the study area, as suggested by the isomeric ratios of PAHs. The results of principal component analysis and multiple linear regressions (PCA/MLR) showed that three sources contributed to the PAHs in the study area, including biomass and coal combustion (48.46%), raw coal (35.49%), and vehicular emission (16.05%). The high value of total benzo[a]pyrene equivalent concentration (B[a]Peq) suggests that local residents are exposed to a high carcinogenic potential.

Assessment of polycyclic aromatic hydrocarbons (PAHs) pollution in soil of suburban areas in Tianjin, China.

PubMed

Lv, Jungang; Shi, Rongguang; Cai, Yanming; Liu, Yong

2010-07-01

Soil contamination with polycyclic aromatic hydrocarbons is an increasing problem and has aroused more and more concern in many countries, including China. In this study, representative soil samples (n = 87) of suburban areas in Tianjin (Xiqing, Dongli, Jinnan, Beichen) were evaluated for 16 polycyclic aromatic hydrocarbons. Surface soil samples were air-dried and sieved. Microwave assisted extraction was used for polycyclic aromatic hydrocarbons preparation prior to analysis with gas chromatography-mass spectrometry. The total concentrations of tested polycyclic aromatic hydrocarbons in Xiqing, Dongli, Jinnan, Beichen ranged in 58.5-2,748.3, 36.1-6,734.7, 58.5-4,502.5, 29.7-852.5 ng/g and the averages of total concentration of polycyclic aromatic hydrocarbons were 600.5, 933.6, 640.8, 257.3 ng/g, respectively. Spatial variation of polycyclic aromatic hydrocarbons in soil was illustrated; Pollution status and comparison to other cities were also investigated. Serious polycyclic aromatic hydrocarbons soil pollution was found in Dongli district, on the contrary, Bap in most sites in Beichen did not exceed relative standards and most sites in Beichen should be classified as non-contaminated soil. Principal component analysis was used to identify the possible sources of different districts. It turned out that coal combustion still was the most important sources in three districts except Beichen. Coking, traffic, cooking, biomass combustion also accounted for polycyclic aromatic hydrocarbons pollution to certain extent in different districts. These data can be further used to assess the health risk associated with soils polluted with polycyclic aromatic hydrocarbons and help local government find proper way to reduce polycyclic aromatic hydrocarbons pollution in soils.

Ambient aromatic hydrocarbon measurements at Welgegund, South Africa

NASA Astrophysics Data System (ADS)

Jaars, K.; Beukes, J. P.; van Zyl, P. G.; Venter, A. D.; Josipovic, M.; Pienaar, J. J.; Vakkari, V.; Aaltonen, H.; Laakso, H.; Kulmala, M.; Tiitta, P.; Guenther, A.; Hellén, H.; Laakso, L.; Hakola, H.

2014-07-01

Aromatic hydrocarbons are associated with direct adverse human health effects and can have negative impacts on ecosystems due to their toxicity, as well as indirect negative effects through the formation of tropospheric ozone and secondary organic aerosol, which affect human health, crop production and regional climate. Measurements of aromatic hydrocarbons were conducted at the Welgegund measurement station (South Africa), which is considered to be a regionally representative background site. However, the site is occasionally impacted by plumes from major anthropogenic source regions in the interior of South Africa, which include the western Bushveld Igneous Complex (e.g. platinum, base metal and ferrochrome smelters), the eastern Bushveld Igneous Complex (platinum and ferrochrome smelters), the Johannesburg-Pretoria metropolitan conurbation (> 10 million people), the Vaal Triangle (e.g. petrochemical and pyrometallurgical industries), the Mpumalanga Highveld (e.g. coal-fired power plants and petrochemical industry) and also a region of anticyclonic recirculation of air mass over the interior of South Africa. The aromatic hydrocarbon measurements were conducted with an automated sampler on Tenax-TA and Carbopack-B adsorbent tubes with heated inlet for 1 year. Samples were collected twice a week for 2 h during daytime and 2 h during night-time. A thermal desorption unit, connected to a gas chromatograph and a mass selective detector was used for sample preparation and analysis. Results indicated that the monthly median (mean) total aromatic hydrocarbon concentrations ranged between 0.01 (0.011) and 3.1 (3.2) ppb. Benzene levels did not exceed the local air quality standard limit, i.e. annual mean of 1.6 ppb. Toluene was the most abundant compound, with an annual median (mean) concentration of 0.63 (0.89) ppb. No statistically significant differences in the concentrations measured during daytime and night-time were found, and no distinct seasonal patterns were

Polyphenylquinoxalines via Aromatic Nucleophilic Displacement

NASA Technical Reports Server (NTRS)

Hergenrother, Paul M.; Connell, John W.

1988-01-01

Polyphenylquinoxalines are produced by an aromatic nucleophilic displacement reaction involving an activated aromatic dihalide with an appropriate quinoxaline monomer. Polyphenylquinoxalines are high temperature thermoplastics used as adhesives, coatings, films and composite matrices. The novelty of this invention is threefold: (1) some of the quinoxaline monomers are new compositions of matter; (2) the phenylquinoxaline polymers which are the end products of the invention are new compositions of matter; and (3) the method of forming the polymers is novel, replacing a more costly prior art process, which is also limited in the kinds of products prepared therefrom.

Ring flips revisited: (13)C relaxation dispersion measurements of aromatic side chain dynamics and activation barriers in basic pancreatic trypsin inhibitor.

PubMed

Weininger, Ulrich; Modig, Kristofer; Akke, Mikael

2014-07-22

Intramolecular motions of proteins are critical for biological function. Transient structural fluctuations underlie a wide range of processes, including enzyme catalysis, ligand binding to buried sites, and generic protein motions, such as 180° rotation of aromatic side chains in the protein interior, but remain poorly understood. Understanding the dynamics and molecular nature of concerted motions requires characterization of their rates and energy barriers. Here we use recently developed (13)C transverse relaxation dispersion methods to improve our current understanding of aromatic ring flips in basic pancreatic trypsin inhibitor (BPTI). We validate these methods by benchmarking ring-flip rates against the three previously characterized cases in BPTI, namely, Y23, Y35, and F45. Further, we measure conformational exchange for one additional aromatic ring, F22, which can be interpreted in terms of a flip rate of 666 s(-1) at 5 °C. Upon inclusion of our previously reported result that Y21 also flips slowly [Weininger, U., et al. (2013) J. Phys. Chem. B 117, 9241-9247], the (13)C relaxation dispersion experiments thus reveal relatively slow ring-flip rates for five of eight aromatic residues in BPTI. These results are in contrast with previous reports, which have estimated that all rings, except Y23, Y35, and F45, flip with a high rate at ambient temperature. The (13)C relaxation dispersion data result in an updated rank order of ring-flip rates in BPTI, which agrees considerably better with that estimated from a recent 1 ms molecular dynamics trajectory than do previously published NMR data. However, significant quantitative differences remain between experiment and simulation, in that the latter yields flip rates that are in many cases too fast by 1-2 orders of magnitude. By measuring flip rates across a temperature range of 5-65 °C, we determined the activation barriers of ring flips for Y23, Y35, and F45. Y23 and F45 have identical activation parameters

Poly(N-arylenebenzimidazole)s via aromatic nucleophilic displacement

NASA Technical Reports Server (NTRS)

Connell, John W. (Inventor); Hergenrother, Paul M. (Inventor); Smith, Jr., Joseph G. (Inventor)

1996-01-01

Novel poly(N-arylenebenzimidazole)s (PNABls) are prepared by the aromatic nucleophilic displacement reaction of novel di(hydroxyphenyl-N-arylene benzimidazole) monomers with activated aromatic dihalides or activated aromatic dinitro compounds. The polymerizations are carried out in polar aprotic solvents such as N-methyl-2-pyrrolidinone or N,N-dimethylacetamide using alkali metal bases such as potassium carbonate at elevated temperatures under nitrogen. The di(hydroxyphenyl-N-arylenebenzimidazole) monomers are synthesized by reacting phenyl-4-hydroxybenzoate with bis(2-aminoanilino)arylenes in diphenylsulfone. Moderate molecular weight PNABIs of new chemical structures were prepared that exhibit a favorable combination of physical and mechanical properties. The use of the novel di(hydroxyphenyI-N-arylenebenzimidazole)s permits a more economical and easier way to prepare PNABIs than previous routes.

Strong Enrichment of Aromatic Residues in Binding Sites from a Charge-neutralized Hyperthermostable Sso7d Scaffold Library*

PubMed Central

Kiefer, Jonathan D.; Srinivas, Raja R.; Lobner, Elisabeth; Tisdale, Alison W.; Mehta, Naveen K.; Yang, Nicole J.; Tidor, Bruce; Wittrup, K. Dane

2016-01-01

The Sso7d protein from the hyperthermophilic archaeon Sulfolobus solfataricus is an attractive binding scaffold because of its small size (7 kDa), high thermal stability (Tm of 98 °C), and absence of cysteines and glycosylation sites. However, as a DNA-binding protein, Sso7d is highly positively charged, introducing a strong specificity constraint for binding epitopes and leading to nonspecific interaction with mammalian cell membranes. In the present study, we report charge-neutralized variants of Sso7d that maintain high thermal stability. Yeast-displayed libraries that were based on this reduced charge Sso7d (rcSso7d) scaffold yielded binders with low nanomolar affinities against mouse serum albumin and several epitopes on human epidermal growth factor receptor. Importantly, starting from a charge-neutralized scaffold facilitated evolutionary adaptation of binders to differentially charged epitopes on mouse serum albumin and human epidermal growth factor receptor, respectively. Interestingly, the distribution of amino acids in the small and rigid binding surface of enriched rcSso7d-based binders is very different from that generally found in more flexible antibody complementarity-determining region loops but resembles the composition of antibody-binding energetic hot spots. Particularly striking was a strong enrichment of the aromatic residues Trp, Tyr, and Phe in rcSso7d-based binders. This suggests that the rigidity and small size of this scaffold determines the unusual amino acid composition of its binding sites, mimicking the energetic core of antibody paratopes. Despite the high frequency of aromatic residues, these rcSso7d-based binders are highly expressed, thermostable, and monomeric, suggesting that the hyperstability of the starting scaffold and the rigidness of the binding surface confer a high tolerance to mutation. PMID:27582495

Strong Enrichment of Aromatic Residues in Binding Sites from a Charge-neutralized Hyperthermostable Sso7d Scaffold Library.

PubMed

Traxlmayr, Michael W; Kiefer, Jonathan D; Srinivas, Raja R; Lobner, Elisabeth; Tisdale, Alison W; Mehta, Naveen K; Yang, Nicole J; Tidor, Bruce; Wittrup, K Dane

2016-10-21

The Sso7d protein from the hyperthermophilic archaeon Sulfolobus solfataricus is an attractive binding scaffold because of its small size (7 kDa), high thermal stability (T m of 98 °C), and absence of cysteines and glycosylation sites. However, as a DNA-binding protein, Sso7d is highly positively charged, introducing a strong specificity constraint for binding epitopes and leading to nonspecific interaction with mammalian cell membranes. In the present study, we report charge-neutralized variants of Sso7d that maintain high thermal stability. Yeast-displayed libraries that were based on this reduced charge Sso7d (rcSso7d) scaffold yielded binders with low nanomolar affinities against mouse serum albumin and several epitopes on human epidermal growth factor receptor. Importantly, starting from a charge-neutralized scaffold facilitated evolutionary adaptation of binders to differentially charged epitopes on mouse serum albumin and human epidermal growth factor receptor, respectively. Interestingly, the distribution of amino acids in the small and rigid binding surface of enriched rcSso7d-based binders is very different from that generally found in more flexible antibody complementarity-determining region loops but resembles the composition of antibody-binding energetic hot spots. Particularly striking was a strong enrichment of the aromatic residues Trp, Tyr, and Phe in rcSso7d-based binders. This suggests that the rigidity and small size of this scaffold determines the unusual amino acid composition of its binding sites, mimicking the energetic core of antibody paratopes. Despite the high frequency of aromatic residues, these rcSso7d-based binders are highly expressed, thermostable, and monomeric, suggesting that the hyperstability of the starting scaffold and the rigidness of the binding surface confer a high tolerance to mutation. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Fusing porphyrins with polycyclic aromatic hydrocarbons and heterocycles for optoelectronic applications

DOEpatents

Thompson, Mark E.; Diev, Viacheslav; Hanson, Kenneth; Forrest, Stephen R.

2015-08-18

A compound that can be used as a donor material in organic photovoltaic devices comprising a non-activated porphyrin fused with one or more non-activated polycyclic aromatic rings or one or more non-activated heterocyclic rings can be obtained by a thermal fusion process. The compounds can include structures of Formula I: ##STR00001## By heating the reaction mixture of non-activated porphyrins with non-activated polycyclic aromatic rings or heterocyclic rings to a fusion temperature and holding for a predetermined time, fusion of one or more polycyclic rings or heterocyclic rings to the non-activated porphyrin core in meso,.beta. fashion is achieved resulting in hybrid structures containing a distorted porphyrin ring with annulated aromatic rings. The porphyrin core can be olygoporphyrins.

Supramolecular aromaticity

NASA Astrophysics Data System (ADS)

Karabıyık, Hande; Sevinçek, Resul; Karabıyık, Hasan

2014-05-01

We report experimental and theoretical evidences for supramolecular aromaticity as a new concept to be widely used in researches about molecular crystals. CSD survey regarding frequently encountered resonance-assisted H-bonds (RAHBs) in formic acid, formamide, formimidamide, formic acid-formamide, and formamide-formimidamide dimers shows that supramolecular quasirings formed by RAHBs have remarkable electronic delocalization within themselves, which is reminiscent of aromaticity at supramolecular level. This study criticizes and reevaluates the validity of conventional judgment which states that ring systems formed by intermolecular H-bonds cannot be aromatic. Thus, the term aromaticity can be extended to supramolecular systems formed by RAHBs. Supramolecular aromaticity has a multi-fold nature involving both σ- and π-delocalization, and σ-delocalization through RAHBs takes on a task of compensating σ-deficiency within quasirings. Atomic composition in donor-acceptor set of the dimers is descriptive for supramolecular aromaticity. We revised bond-valence parameters for RAHBs and they suggest that hypervalent character of H atoms is more pronounced than their hypovalent character in RAHBs. The σ-delocalized bonding within H-bonded quasirings necessitates hypervalent character of H atoms. Quantum chemical calculations based on adiabatic Hydrogen Atom Transfer (HAT) between the monomers reveal that topological parameters at ring critical points (RCPs) of the quasirings correlate well with Shannon's entropic aromaticity index. The presence of additional LP orbital on O atoms implying more diffused LP-orbitals in donor-acceptor set leads to the formation of resonance-disabling states reducing supramolecular aromaticity of a quasiring and energetic cost of the electron transfer between the monomers. There is a nonignorable electron transfer between the monomers even in the cases where H atoms are close to donor or acceptor atom. NBO analyses have revealed that

Surface chemistry of aromatic reactants on Pt- and Mo-modified Pt catalysts

DOE Office of Scientific and Technical Information (OSTI.GOV)

Robinson, Allison M.; Mark, Lesli; Rasmussen, Mathew J.

Supported catalysts containing an oxophilic metal such as Mo and a noble metal such as Pt have shown promising activity and selectivity for deoxygenation of biomass-derived compounds. Here, we report that PtMo catalysts also promote hydrogenolysis of the model compound benzyl alcohol, while decarbonylation is most prevalent over unmodified Pt. A combination of single crystal surface science studies, density functional theory (DFT) calculations, and vapor phase upgrading experiments using supported catalysts was carried out to better understand the mechanism by which Mo promotes deoxygenation. Molybdenum was deposited in submonolayer quantities on a Pt(111) surface and reduced at high temperature. Temperature-programmedmore » desorption (TPD) experiments using benzyl alcohol as a reactant showed greatly enhanced yields of the deoxygenation product toluene at moderate Mo coverages. To understand how the interaction of the aromatic group with the surface influenced this reactivity, we investigated the adsorption of toluene as a probe molecule. We found that the addition of Mo to Pt(111) resulted in a significant decrease in toluene decomposition. DFT calculations indicated that this decrease was consistent with decreased aromatic adsorption strengths that accompany incorporation of Mo into the Pt subsurface. The weaker aromatic-surface interaction on Pt/Mo surfaces led to a tilted adsorption geometry for benzyl alcohol, which presumably promotes hydrogenolysis to produce toluene instead of decarbonylation to produce benzene and CO. Alumina-supported Pt and PtMo catalysts were also tested for benzyl alcohol deoxygenation. PtMo catalysts had a higher rate of toluene production and lower rates of benzene and benzaldehyde production. Additionally, when benzaldehyde was used as the reactant to measure decarbonylation activity the mass-normalized rate of benzene production was 2.5 times higher on Pt than PtMo. Altogether, the results of TPD, DFT, and supported catalyst

Surface chemistry of aromatic reactants on Pt- and Mo-modified Pt catalysts

DOE PAGES

Robinson, Allison M.; Mark, Lesli; Rasmussen, Mathew J.; ...

2016-11-01

Supported catalysts containing an oxophilic metal such as Mo and a noble metal such as Pt have shown promising activity and selectivity for deoxygenation of biomass-derived compounds. Here, we report that PtMo catalysts also promote hydrogenolysis of the model compound benzyl alcohol, while decarbonylation is most prevalent over unmodified Pt. A combination of single crystal surface science studies, density functional theory (DFT) calculations, and vapor phase upgrading experiments using supported catalysts was carried out to better understand the mechanism by which Mo promotes deoxygenation. Molybdenum was deposited in submonolayer quantities on a Pt(111) surface and reduced at high temperature. Temperature-programmedmore » desorption (TPD) experiments using benzyl alcohol as a reactant showed greatly enhanced yields of the deoxygenation product toluene at moderate Mo coverages. To understand how the interaction of the aromatic group with the surface influenced this reactivity, we investigated the adsorption of toluene as a probe molecule. We found that the addition of Mo to Pt(111) resulted in a significant decrease in toluene decomposition. DFT calculations indicated that this decrease was consistent with decreased aromatic adsorption strengths that accompany incorporation of Mo into the Pt subsurface. The weaker aromatic-surface interaction on Pt/Mo surfaces led to a tilted adsorption geometry for benzyl alcohol, which presumably promotes hydrogenolysis to produce toluene instead of decarbonylation to produce benzene and CO. Alumina-supported Pt and PtMo catalysts were also tested for benzyl alcohol deoxygenation. PtMo catalysts had a higher rate of toluene production and lower rates of benzene and benzaldehyde production. Additionally, when benzaldehyde was used as the reactant to measure decarbonylation activity the mass-normalized rate of benzene production was 2.5 times higher on Pt than PtMo. Altogether, the results of TPD, DFT, and supported catalyst

ATR-FTIR spectroscopy reveals polycyclic aromatic hydrocarbon contamination despite relatively pristine site characteristics: Results of a field study in the Niger Delta.

PubMed

Obinaju, Blessing E; Martin, Francis L

2016-01-01

Fourier-transform infrared (FTIR) spectroscopy is an emerging technique to detect biochemical alterations in biological tissues, particularly changes due to sub-lethal exposures to environmental contaminants. We have previously shown the potential of attenuated total reflection FTIR (ATR-FTIR) spectroscopy to detect real-time exposure to contaminants in sentinel organisms as well as the potential to relate spectral alterations to the presence of specific environmental agents. In this study based in the Niger Delta (Nigeria), changes occurring in fish tissues as a result of polycyclic aromatic hydrocarbon (PAH) exposure at contaminated sites are compared to the infrared (IR) spectra of the tissues obtained from a relatively pristine site. Multivariate analysis revealed that PAH contamination could be occurring at the pristine site, based on the IR spectra and significant (P<0.0001) differences between sites. The study provides evidence of the IR spectroscopy techniques' sensitivity and supports their potential application in environmental biomonitoring. Copyright © 2016 Elsevier Ltd. All rights reserved.

Ligand-binding specificity and promiscuity of the main lignocellulolytic enzyme families as revealed by active-site architecture analysis.

PubMed

Tian, Li; Liu, Shijia; Wang, Shuai; Wang, Lushan

2016-03-24

Biomass can be converted into sugars by a series of lignocellulolytic enzymes, which belong to the glycoside hydrolase (GH) families summarized in CAZy databases. Here, using a structural bioinformatics method, we analyzed the active site architecture of the main lignocellulolytic enzyme families. The aromatic amino acids Trp/Tyr and polar amino acids Glu/Asp/Asn/Gln/Arg occurred at higher frequencies in the active site architecture than in the whole enzyme structure. And the number of potential subsites was significantly different among different families. In the cellulase and xylanase families, the conserved amino acids in the active site architecture were mostly found at the -2 to +1 subsites, while in β-glucosidase they were mainly concentrated at the -1 subsite. Families with more conserved binding amino acid residues displayed strong selectivity for their ligands, while those with fewer conserved binding amino acid residues often exhibited promiscuity when recognizing ligands. Enzymes with different activities also tended to bind different hydroxyl oxygen atoms on the ligand. These results may help us to better understand the common and unique structural bases of enzyme-ligand recognition from different families and provide a theoretical basis for the functional evolution and rational design of major lignocellulolytic enzymes.

Biodegradation of Aromatic Compounds by Escherichia coli

PubMed Central

Díaz, Eduardo; Ferrández, Abel; Prieto, María A.; García, José L.

2001-01-01

Although Escherichia coli has long been recognized as the best-understood living organism, little was known about its abilities to use aromatic compounds as sole carbon and energy sources. This review gives an extensive overview of the current knowledge of the catabolism of aromatic compounds by E. coli. After giving a general overview of the aromatic compounds that E. coli strains encounter and mineralize in the different habitats that they colonize, we provide an up-to-date status report on the genes and proteins involved in the catabolism of such compounds, namely, several aromatic acids (phenylacetic acid, 3- and 4-hydroxyphenylacetic acid, phenylpropionic acid, 3-hydroxyphenylpropionic acid, and 3-hydroxycinnamic acid) and amines (phenylethylamine, tyramine, and dopamine). Other enzymatic activities acting on aromatic compounds in E. coli are also reviewed and evaluated. The review also reflects the present impact of genomic research and how the analysis of the whole E. coli genome reveals novel aromatic catabolic functions. Moreover, evolutionary considerations derived from sequence comparisons between the aromatic catabolic clusters of E. coli and homologous clusters from an increasing number of bacteria are also discussed. The recent progress in the understanding of the fundamentals that govern the degradation of aromatic compounds in E. coli makes this bacterium a very useful model system to decipher biochemical, genetic, evolutionary, and ecological aspects of the catabolism of such compounds. In the last part of the review, we discuss strategies and concepts to metabolically engineer E. coli to suit specific needs for biodegradation and biotransformation of aromatics and we provide several examples based on selected studies. Finally, conclusions derived from this review may serve as a lead for future research and applications. PMID:11729263

Evaluation of heavy metal and polycyclic aromatic hydrocarbons accumulation in plants from typical industrial sites: potential candidate in phytoremediation for co-contamination.

PubMed

Sun, Lu; Liao, Xiaoyong; Yan, Xiulan; Zhu, Ganghui; Ma, Dong

2014-11-01

The heavy metal and polycyclic aromatic hydrocarbons (PAHs) contents were evaluated in surface soil and plant samples of 18 wild species collected from 3 typical industrial sites in South Central China. The accumulative characteristics of the plant species for both heavy metal and PAHs were discussed. The simultaneous accumulation of heavy metal and PAHs in plant and soil was observed at all the investigated sites, although disparities in spatial distributions among sites occurred. Both plant and soil samples were characterized by high accumulation for heavy metal at smelting site, moderate enrichment at coke power and coal mining sites, whereas high level of PAHs (16 priority pollutants according to US Environmental Protection Agency) at coke power site, followed sequentially by coal mining and smelting sites. Based on the differences of heavy metal and PAH accumulation behaviors of the studied plant species, heavy metal and PAH accumulation strategies were suggested: Pteris vittata L. and Pteris cretica L. for As and PAHs, Boehmeria nivea (L.) Gaud for Pb, As, and PAHs, and Miscanthus floridulu (Labnll.) Warb for Cu and PAHs. These native plant species could be proposed as promising materials for heavy metal and PAHs combined pollution remediation.

In situ STM investigation of aromatic poly(azomethine) arrays constructed by "on-site" equilibrium polymerization.

PubMed

Tanoue, Ryota; Higuchi, Rintaro; Ikebe, Kiryu; Uemura, Shinobu; Kimizuka, Nobuo; Stieg, Adam Z; Gimzewski, James K; Kunitake, Masashi

2012-10-02

Two-dimensional (2D) arrays of π-conjugated aromatic polymers produced by surface-selective Schiff base coupling reactions between an aromatic diamine and an aromatic dialdehyde were investigated in detail using in situ scanning tunneling microscopy. Surface-selective coupling was achieved for almost all diamine/dialdehyde combinations attempted, although several combinations did not proceed even in homogeneous aqueous alkaline solution. Most of the combinations of an aromatic diamine and a dialdehyde, except the combinations of 4,4'-azodianiline with mono/bithiophenedicarboxaldehyde, formed highly ordered π-conjugated polymer arrays on an iodine-modified Au(111) surface in aqueous solution at a suitable pH. The simplest polymer of the various combinations tested, obtained from the combination of 1,4-diaminobenzene with terephthaldicarboxaldehyde, gave a 2D array consisting of linearly connected benzene units. Poly(azomethine) adlayers caused a positive shift in the electrochemical potential of the butterfly shaped oxidative adsorption and reductive desorption of iodine. The acceleration of the reductive desorption of iodine suggests the existence of a weak interaction between the polymer layer and iodine. Not only the first polymer adlayers but also partially adsorbed secondary adlayers with "on-top" epitaxial behavior were frequently observed for all polymer systems. The alignment of the polymer chains in the adlayers possessed a certain regularity in terms of a regular interval between polymer chains because of repulsive interpolymer interactions.

Spectroscopic Diagnosis of Excited-State Aromaticity: Capturing Electronic Structures and Conformations upon Aromaticity Reversal.

PubMed

Oh, Juwon; Sung, Young Mo; Hong, Yongseok; Kim, Dongho

2018-03-06

Aromaticity, the special energetic stability derived from cyclic [4 n + 2]π-conjugated electronic structures, has been the topic of intense interest in chemistry because it plays a critical role in rationalizing molecular stability, reactivity, and physical/chemical properties. Recently, the pioneering work by Colin Baird on aromaticity reversal, postulating that aromatic (antiaromatic) character in the ground state reverses to antiaromatic (aromatic) character in the lowest excited triplet state, has attracted much scientific attention. The completely reversed aromaticity in the excited state provides direct insight into understanding the photophysical/chemical properties of photoactive materials. In turn, the application of aromatic molecules to photoactive materials has led to numerous studies revealing this aromaticity reversal. However, most studies of excited-state aromaticity have been based on the theoretical point of view. The experimental evaluation of aromaticity in the excited state is still challenging and strenuous because the assessment of (anti)aromaticity with conventional magnetic, energetic, and geometric indices is difficult in the excited state, which practically restricts the extension and application of the concept of excited-state aromaticity. Time-resolved optical spectroscopies can provide a new and alternative avenue to evaluate excited-state aromaticity experimentally while observing changes in the molecular features in the excited states. Time-resolved optical spectroscopies take advantage of ultrafast laser pulses to achieve high time resolution, making them suitable for monitoring ultrafast changes in the excited states of molecular systems. This can provide valuable information for understanding the aromaticity reversal. This Account presents recent breakthroughs in the experimental assessment of excited-state aromaticity and the verification of aromaticity reversal with time-resolved optical spectroscopic measurements. To

Himalayan Aromatic Medicinal Plants: A Review of their Ethnopharmacology, Volatile Phytochemistry, and Biological Activities

PubMed Central

Joshi, Rakesh K.; Satyal, Prabodh; Setzer, Wiliam N.

2016-01-01

Aromatic plants have played key roles in the lives of tribal peoples living in the Himalaya by providing products for both food and medicine. This review presents a summary of aromatic medicinal plants from the Indian Himalaya, Nepal, and Bhutan, focusing on plant species for which volatile compositions have been described. The review summarizes 116 aromatic plant species distributed over 26 families. PMID:28930116

Synthesis of Novel Aza-aromatic Curcuminoids with Improved Biological Activities towards Various Cancer Cell Lines.

PubMed

Theppawong, Atiruj; Van de Walle, Tim; Grootaert, Charlotte; Bultinck, Margot; Desmet, Tom; Van Camp, John; D'hooghe, Matthias

2018-05-01

Curcumin, a natural compound extracted from the rhizomes of Curcuma longa , displays pronounced anticancer properties but lacks good bioavailability and stability. In a previous study, we initiated structure modification of the curcumin scaffold by imination of the labile β-diketone moiety to produce novel β-enaminone derivatives. These compounds showed promising properties for elaborate follow-up studies. In this work, we focused on another class of nitrogen-containing curcuminoids with a similar objective: to address the bioavailability and stability issues and to improve the biological activity of curcumin. This paper thus reports on the synthesis of new pyridine-, indole-, and pyrrole-based curcumin analogues (aza-aromatic curcuminoids) and discusses their water solubility, antioxidant activity, and antiproliferative properties. In addition, multivariate statistics, including hierarchical clustering analysis and principal component analysis, were performed on a broad set of nitrogen-containing curcuminoids. Compared to their respective mother structures, that is, curcumin and bisdemethoxycurcumin, all compounds, and especially the pyridin-3-yl β-enaminone analogues, showed better water solubility profiles. Interestingly, the pyridine-, indole-, and pyrrole-based curcumin derivatives demonstrated improved biological effects in terms of mitochondrial activity impairment and protein content, in addition to comparable or decreased antioxidant properties. Overall, the biologically active N -alkyl β-enaminone aza-aromatic curcuminoids were shown to offer a desirable balance between good solubility and significant bioactivity.

Fluorinated Aromatic Amino Acids Distinguish Cation-π Interactions from Membrane Insertion*

PubMed Central

He, Tao; Gershenson, Anne; Eyles, Stephen J.; Lee, Yan-Jiun; Liu, Wenshe R.; Wang, Jiangyun; Gao, Jianmin; Roberts, Mary F.

2015-01-01

Cation-π interactions, where protein aromatic residues supply π systems while a positive-charged portion of phospholipid head groups are the cations, have been suggested as important binding modes for peripheral membrane proteins. However, aromatic amino acids can also insert into membranes and hydrophobically interact with lipid tails. Heretofore there has been no facile way to differentiate these two types of interactions. We show that specific incorporation of fluorinated amino acids into proteins can experimentally distinguish cation-π interactions from membrane insertion of the aromatic side chains. Fluorinated aromatic amino acids destabilize the cation-π interactions by altering electrostatics of the aromatic ring, whereas their increased hydrophobicity enhances membrane insertion. Incorporation of pentafluorophenylalanine or difluorotyrosine into a Staphylococcus aureus phosphatidylinositol-specific phospholipase C variant engineered to contain a specific PC-binding site demonstrates the effectiveness of this methodology. Applying this methodology to the plethora of tyrosine residues in Bacillus thuringiensis phosphatidylinositol-specific phospholipase C definitively identifies those involved in cation-π interactions with phosphatidylcholine. This powerful method can easily be used to determine the roles of aromatic residues in other peripheral membrane proteins and in integral membrane proteins. PMID:26092728

Polyimidazoles Via Aromatic Nucleophilic Displacement

NASA Technical Reports Server (NTRS)

Connell, John W.; Hergenrother, Paul M.

1990-01-01

Experiments show variety of polyimidazoles prepared by aromatic nucleophilic displacement, from reactions of bisphenol imidazoles with activated difluoro compounds. Polyimidazoles have good mechanical properties making them suitable for use as films, moldings, and adhesives.

Bisphenol-A alters microbiota metabolites derived from aromatic amino acids and worsens disease activity during colitis.

PubMed

DeLuca, Jennifer Aa; Allred, Kimberly F; Menon, Rani; Riordan, Rebekah; Weeks, Brad R; Jayaraman, Arul; Allred, Clinton D

2018-06-01

Inflammatory bowel disease is a complex collection of disorders. Microbial dysbiosis as well as exposure to toxins including xenoestrogens are thought to be risk factors for inflammatory bowel disease development and relapse. Bisphenol-A has been shown to exert estrogenic activity in the colon and alter intestinal function, but the role that xenoestrogens, such as bisphenol-A , play in colonic inflammation has been previously described but with conflicting results. We investigated the ability of bisphenol-A to exacerbate colonic inflammation and alter microbiota metabolites derived from aromatic amino acids in an acute dextran sulfate sodium-induced colitis model. Female C57BL/6 mice were ovariectomized and exposed to bisphenol-A daily for 15 days. Disease activity measures include body weight, fecal consistency, and rectal bleeding. Colons were scored for inflammation, injury, and nodularity. Alterations in the levels of microbiota metabolites derived from aromatic amino acids known to reflect phenotypic changes in the gut microbiome were analyzed. Bisphenol-A exposure increased mortality and worsened disease activity as well as inflammation and nodularity scores in the middle colon region following dextran sulfate sodium exposure. Unique patterns of metabolites were associated with bisphenol-A consumption. Regardless of dextran sulfate sodium treatment, bisphenol-A reduced levels of tryptophan and several metabolites associated with decreased inflammation in the colon. This is the first study to show that bisphenol-A treatment alone can reduce microbiota metabolites derived from aromatic amino acids in the colon which may be associated with increased colonic inflammation and inflammatory bowel disease. Impact statement As rates of inflammatory bowel disease rise, discovery of the mechanisms related to the development of these conditions is important. Environmental exposure is hypothesized to play a role in etiology of the disease, as are alterations in the gut

Revealing potential functions of VBNC bacteria in polycyclic aromatic hydrocarbons biodegradation.

PubMed

Su, X M; Bamba, A M; Zhang, S; Zhang, Y G; Hashmi, M Z; Lin, H J; Ding, L X

2018-04-01

The bioremediation of polycyclic aromatic hydrocarbon (PAH)-contaminated sites is not running smoothly, because of the lower activity of PAH-degrading bacteria in actual bioremediation applications. The phenomenon of "viable but nonculturable" (VBNC) state may be a main limiting factor for their poor biodegradation capabilities of PAHs. Due to their abilities of entering into the VBNC state, most of bacterial populations with PAH-degradation potential remain unculturable. Resuscitation of VBNC bacteria will enhance the degradation capability of indigenous bacteria which will eventually obtain their better capabilities in environmental bioremediation. Although evidences have been presented indicating that resuscitation of VBNC bacteria in polychlorinated biphenyl (PCB)-contaminated environments not only significantly enhanced PCB degradation, but also obtained novel highly efficient PCB-degrading bacteria, scanty information is available on the VBNC bacteria in PAH-contaminated sites. VBNC bacteria, as a vast majority of potential microbial resource could be the repository of novel highly efficient PAH-biodegraders. Therefore, studies need to be done on resuscitation of VBNC bacteria to overcome key bottlenecks in bioremediation of PAH-contaminated sites. This mini-review provides a new insight into the potential functions of VBNC bacteria in PAHs biodegradation. As the vast majority microbial resource, viable but nonculturable (VBNC) bacteria, which showed their potential functions in polycyclic aromatic hydrocarbons (PAHs) biodegradation, can be of great significance in environmental bioremediation. It is therefore important to resuscitate VBNC bacteria for their better capabilities. Meanwhile, preventing the indigenous functional community from entering into the VBNC state will also maintain the high activity of PAH-degrading bacteria in actual bioremediation applications. Undoubtedly, much more work needs to be done to reveal indigenous micro-organisms in the

Aromatic residues located close to the active center are essential for the catalytic reaction of flap endonuclease-1 from hyperthermophilic archaeon Pyrococcus horikoshii.

PubMed

Matsui, Eriko; Abe, Junko; Yokoyama, Hideshi; Matsui, Ikuo

2004-04-16

Flap endonuclease-1 (FEN-1) possessing 5'-flap endonuclease and 5'-->3' exonuclease activity plays important roles in DNA replication and repair. In this study, the kinetic parameters of mutants at highly conserved aromatic residues, Tyr33, Phe35, Phe79, and Phe278-Phe279, in the vicinity of the catalytic centers of FEN-1 were examined. The substitution of these aromatic residues with alanine led to a large reduction in kcat values, although these mutants retained Km values similar to that of the wild-type enzyme. Notably, the kcat of Y33A and F79A decreased 333-fold and 71-fold, respectively, compared with that of the wild-type enzyme. The aromatic residues Tyr33 and Phe79, and the aromatic cluster Phe278-Phe279 mainly contributed to the recognition of the substrates without the 3' projection of the upstream strand (the nick, 5'-recess-end, single-flap, and pseudo-Y substrates) for the both exo- and endo-activities, but played minor roles in recognizing the substrates with the 3' projection (the double flap substrate and the nick substrate with the 3' projection). The replacement of Tyr33, Phe79, and Phe278-Phe279, with non-charged aromatic residues, but not with aliphatic hydrophobic residues, recovered the kcat values almost fully for the substrates without the 3' projection of the upstream strand, suggesting that the aromatic groups of Tyr33, Phe79, and Phe278-Phe279 might be involved in the catalytic reaction, probably via multiple stacking interactions with nucleotide bases. The stacking interactions of Tyr33 and Phe79 might play important roles in fixing the template strand and the downstream strand, respectively, in close proximity to the active center to achieve the productive transient state leading to the hydrolysis.

Measurements of gas and particle polycyclic aromatic hydrocarbons (PAHs) in air at urban, rural and near-roadway sites

NASA Astrophysics Data System (ADS)

Pratt, G. C.; Herbrandson, C.; Krause, M. J.; Schmitt, C.; Lippert, C. J.; McMahon, C. R.; Ellickson, K. M.

2018-04-01

We measured polycyclic aromatic hydrocarbons (PAHs) in gas and particle phases over two years using high volume samplers equipped with quartz fiber filters and XAD-4 at a rural site, an urban site, and a site adjacent to a heavily trafficked roadway. Overall results were generally as expected, in that concentrations increased from rural to urban to near-roadway sites, and PAHs with high vapor pressures (liquid subcooled, PoL) and low octanol-air partition coefficients (Koa) were mainly in the gas phase, while those with low PoL and high Koa were predominantly in the particle phase. Intermediate PAHs existed in both phases with the phase distribution following a seasonal pattern of higher gas phase concentrations in summer due to temperature effects. The overall pattern of phase distribution was consistent with PAH properties and ambient conditions and was similar at all three sites. The particle-bound fraction (ϕ) was well-described empirically by nonlinear regressions with log Koa and log PoL as predictors. Adsorption and absorption models underestimated the particle-bound fraction for most PAHs. The dual aerosol-air/soot-air model generally represented the gas-particle partitioning better than the other models across all PAHs, but there was a tendency to underestimate the range in the particle-bound fraction seen in measurements. There was a statistically insignificant tendency for higher PAHs in the particle phase at the near roadway site, and one piece of evidence that PAHs may be enriched on ultrafine particles at the near roadway site. Understanding the phase and particle size distributions of PAHs in highly polluted, high exposure microenvironments near traffic sources will help shed light on potential health effects.

Aromatic Polyimide Foam

NASA Technical Reports Server (NTRS)

Weiser, Erik S. (Inventor); St.Clair, Terry L. (Inventor); Echigo, Yoshiaki (Inventor); Kaneshiro, Hisayasu (Inventor)

2000-01-01

A mechanically undensified aromatic polyimide foam is made from an aromatic polyimide precursor solid residuum and has the following combination of properties: a density according to ASTM D-3574A of about 0.5 pounds/cu.ft to about 20 pounds/cu.ft; a compression strength according to ASTM D-3574C of about 1.5 psi to about 1500 psi; and a limiting oxygen index according to ASTM D-2863 of about 35% oxygen to about 75% oxygen at atmospheric pressure. The aromatic polyimide foam has no appreciable solid inorganic contaminants which are residues of inorganic blowing agents. The aromatic polyimide which constitutes the aromatic polyimide foam has a glass transition temperature (Tg) by differential scanning calorimetry of about 235 C to about 400 C; and a thermal stability of 0 to about 1% weight loss at 204 C as determined by thermogravinietric analysis (TGA). The aromatic polyimide foam has utility as foam insulation and as structural foam, for example, for aeronautical, aerospace and maritime applications.

(Hetero)aromatics from dienynes, enediynes and enyne-allenes.

PubMed

Raviola, Carlotta; Protti, Stefano; Ravelli, Davide; Fagnoni, Maurizio

2016-08-07

The construction of aromatic rings has become a key objective for organic chemists. While several strategies have been developed for the functionalization of pre-formed aromatic rings, the direct construction of an aromatic core starting from polyunsaturated systems is yet a less explored field. The potential of such reactions in the formation of aromatics increased at a regular pace in the last few years. Nowadays, there are reliable and well-established procedures to prepare polyenic derivatives, such as dienynes, enediynes, enyne-allenes and hetero-analogues. This has stimulated their use in the development of innovative cycloaromatizations. Different examples have recently emerged, suggesting large potential of this strategy in the preparation of (hetero)aromatics. Accordingly, this review highlights the recent advancements in this field and describes the different conditions exploited to trigger the process, including thermal and photochemical activation, as well as the use of transition metal catalysis and the addition of electrophiles/nucleophiles or radical species.

Atypical kinetic behavior of chloroperoxidase-mediated oxidative halogenation of polycyclic aromatic hydrocarbons.

PubMed

Aburto, Jorge; Correa-Basurto, Jose; Torres, Eduardo

2008-12-01

We have identified an atypical kinetic behavior for the oxidative halogenation of several polycyclic aromatic hydrocarbons (PAHs) by chloroperoxidase (CPO) from Caldariomyces fumago. This behavior resembles the capacity of some members of the P450 family to simultaneously recognize several substrate molecules at their active sites. Indeed, fluorometric studies showed that PAHs exist in solution as monomers and pi-pi dimers that interact to different extents with CPO. The dissociation constants of dimerization were evaluated for every single PAH by spectrofluorometry. Furthermore, docking studies also suggest that CPO might recognize either one or two substrate molecules in its active site. The atypical sigmoidal kinetic behavior of CPO in the oxidative halogenation of PAHs is explained in terms of different kinetic models for non-heteroatomic PAHs (naphthalene, anthracene and pyrene). The results suggest that the actual substrate for CPO in this study was the pi-pi dimer for all evaluated PAHs.

Experimental warming differentially affects microbial structure and activity in two contrasted moisture sites in a Sphagnum-dominated peatland.

PubMed

Delarue, Frédéric; Buttler, Alexandre; Bragazza, Luca; Grasset, Laurent; Jassey, Vincent E J; Gogo, Sébastien; Laggoun-Défarge, Fatima

2015-04-01

Several studies on the impact of climate warming have indicated that peat decomposition/mineralization will be enhanced. Most of these studies deal with the impact of experimental warming during summer when prevalent abiotic conditions are favorable to decomposition. Here, we investigated the effect of experimental air warming by open-top chambers (OTCs) on water-extractable organic matter (WEOM), microbial biomasses and enzymatic activities in two contrasted moisture sites named Bog and Fen sites, the latter considered as the wetter ones. While no or few changes in peat temperature and water content appeared under the overall effect of OTCs, we observed that air warming smoothed water content differences and led to a decrease in mean peat temperature at the warmed Bog sites. This thermal discrepancy between the two sites led to contrasting changes in microbial structure and activities: a rise in hydrolytic activity at the warmed Bog sites and a relative enhancement of bacterial biomass at the warmed Fen sites. These features were not associated with any change in WEOM properties namely carbon and sugar contents and aromaticity, suggesting that air warming did not trigger any shift in OM decomposition. Using various tools, we show that the use of single indicators of OM decomposition can lead to fallacious conclusions. Lastly, these patterns may change seasonally as a consequence of complex interactions between groundwater level and air warming, suggesting the need to improve our knowledge using a high time-resolution approach. Copyright © 2015 Elsevier B.V. All rights reserved.

Improvement of aromatic thiol release through the selection of yeasts with increased β-lyase activity.

PubMed

Belda, Ignacio; Ruiz, Javier; Navascués, Eva; Marquina, Domingo; Santos, Antonio

2016-05-16

The development of a selective medium for the rapid differentiation of yeast species with increased aromatic thiol release activity has been achieved. The selective medium was based on the addition of S-methyl-l-cysteine (SMC) as β-lyase substrate. In this study, a panel of 245 strains of Saccharomyces cerevisiae strains was tested for their ability to grow on YCB-SMC medium. Yeast strains with an increased β-lyase activity grew rapidly because of their ability to release ammonium from SMC in comparison to others, and allowed for the easy isolation and differentiation of yeasts with promising properties in oenology, or another field, for aromatic thiol release. The selective medium was also helpful for the discrimination between those S. cerevisiae strains, which present a common 38-bp deletion in the IRC7 sequence (present in around 88% of the wild strains tested and are likely to be less functional for 4-mercapto-4-methylpentan-2-one (4MMP) production), and those S. cerevisiae strains homozygous for the full-length IRC7 allele. The medium was also helpful for the selection of non-Saccharomyces yeasts with increased β-lyase activity. Based on the same medium, a highly sensitive, reproducible and non-expensive GC-MS method for the evaluation of the potential volatile thiol release by different yeast isolates was developed. Copyright © 2016 Elsevier B.V. All rights reserved.

Oxidation of aromatic contaminants coupled to microbial iron reduction

USGS Publications Warehouse

Lovley, D.R.; Baedecker, M.J.; Lonergan, D.J.; Cozzarelli, I.M.; Phillips, E.J.P.; Siegel, D.I.

1989-01-01

THE contamination of sub-surface water supplies with aromatic compounds is a significant environmental concern1,2. As these contaminated sub-surface environments are generally anaerobic, the microbial oxidation of aromatic compounds coupled to nitrate reduction, sulphate reduction and methane production has been studied intensively1-7. In addition, geochemical evidence suggests that Fe(III) can be an important electron acceptor for the oxidation of aromatic compounds in anaerobic groundwater. Until now, only abiological mechanisms for the oxidation of aromatic compounds with Fe(III) have been reported8-12. Here we show that in aquatic sediments, microbial activity is necessary for the oxidation of model aromatic compounds coupled to Fe(III) reduction. Furthermore, a pure culture of the Fe(III)-reducing bacterium GS-15 can obtain energy for growth by oxidizing benzoate, toluene, phenol or p-cresol with Fe(III) as the sole electron acceptor. These results extend the known physiological capabilities of Fe(III)-reducing organisms and provide the first example of an organism of any type which can oxidize an aromatic hydrocarbon anaerobically. ?? 1989 Nature Publishing Group.

Effect of ZSM-5 acidity on aromatic product selectivity during upgrading of pine pyrolysis vapors

DOE PAGES

Engtrakul, Chaiwat; Mukarakate, Calvin; Starace, Anne K.; ...

2015-11-14

The impact of catalyst acidity on the selectivity of upgraded biomass pyrolysis products was studied by passing pine pyrolysis vapors over five ZSM-5 catalysts of varying acidity at 500 degrees C. The SiO 2-to-Al 2O 3 ratio (SAR) of the ZSM-5 zeolite was varied from 23 to 280 to control the acidity of the catalyst and the composition of upgraded products. The upgraded product stream was analyzed by GCMS. Additionally, catalysts were characterized using temperature programmed desorption, diffuse-reflectance FTIR spectroscopy, N 2 physisorption, and X-ray diffraction. The results showed that the biomass pyrolysis vapors were highly deoxygenated to form amore » slate of aromatic hydrocarbons over all of the tested ZSM-5 catalysts. As the overall acidity of the ZSM-5 increased the selectivity toward alkylated (substituted) aromatics (e.g., xylene, dimethyl-naphthalene, and methyl-anthracene) decreased while the selectivity toward unsubstituted aromatics (e.g., benzene, naphthalene, and anthracene) increased. Additionally, the selectivity toward polycyclic aromatic compounds (2-ring and 3-ring) increased as catalyst acidity increased, corresponding to a decrease in acid site spacing. The increased selectivity toward less substituted polycyclic aromatic compounds with increasing acidity is related to the relative rates of cyclization and alkylation reactions within the zeolite structure. As the acid site concentration increases and sites become closer to each other, the formation of additional cyclization products occurs at a greater rate than alkylated products. The ability to adjust product selectivity within 1-, 2-, and 3-ring aromatic families, as well as the degree of substitution, by varying ZSM-5 acidity could have significant benefits in terms creating a slate of upgraded biomass pyrolysis products to meet specific target market demands.« less

A Survey of Chemical Compositions and Biological Activities of Yemeni Aromatic Medicinal Plants

PubMed Central

Chhetri, Bhuwan K.; Awadh Ali, Nasser A.; Setzer, William N.

2015-01-01

Yemen is a small country located in the southwestern part of the Arabian Peninsula. Yemen’s coastal lowlands, eastern plateau, and deserts give it a diverse topography, which along with climatic factors make it opulent in flora. Despite the introduction of Western medicinal system during the middle of the twentieth century, herbal medicine still plays an important role in Yemen. In this review, we present a survey of several aromatic plants used in traditional medicine in Yemen, their traditional uses, their volatile chemical compositions, and their biological activities. PMID:28930202

Adsorption of aromatic compounds from the biodegradation of azo dyes on activated carbon

NASA Astrophysics Data System (ADS)

Faria, P. C. C.; Órfão, J. J. M.; Figueiredo, J. L.; Pereira, M. F. R.

2008-03-01

The adsorption of three selected aromatic compounds (aniline, sulfanilic acid and benzenesulfonic acid) on activated carbons with different surface chemical properties was investigated at different solution pH. A fairly basic commercial activated carbon was modified by means of chemical treatment with HNO 3, yielding an acid activated carbon. The textural properties of this sample were not significantly changed after the oxidation treatment. Equilibrium isotherms of the selected compounds on the mentioned samples were obtained and the results were discussed in relation to their surface chemistry. The influence of electrostatic and dispersive interactions involved in the uptake of the compounds studied was evaluated. The Freundlich model was used to fit the experimental data. Higher uptakes are attained when the compounds are present in their molecular form. In general, adsorption was disfavoured by the introduction of oxygen-containing groups on the surface of the activated carbon.

An Aromatic Sensor with Aversion to Damaged Strands Confers Versatility to DNA Repair

PubMed Central

Maillard, Olivier; Solyom, Szilvia; Naegeli, Hanspeter

2007-01-01

It was not known how xeroderma pigmentosum group C (XPC) protein, the primary initiator of global nucleotide excision repair, achieves its outstanding substrate versatility. Here, we analyzed the molecular pathology of a unique Trp690Ser substitution, which is the only reported missense mutation in xeroderma patients mapping to the evolutionary conserved region of XPC protein. The function of this critical residue and neighboring conserved aromatics was tested by site-directed mutagenesis followed by screening for excision activity and DNA binding. This comparison demonstrated that Trp690 and Phe733 drive the preferential recruitment of XPC protein to repair substrates by mediating an exquisite affinity for single-stranded sites. Such a dual deployment of aromatic side chains is the distinctive feature of functional oligonucleotide/oligosaccharide-binding folds and, indeed, sequence homologies with replication protein A and breast cancer susceptibility 2 protein indicate that XPC displays a monomeric variant of this recurrent interaction motif. An aversion to associate with damaged oligonucleotides implies that XPC protein avoids direct contacts with base adducts. These results reveal for the first time, to our knowledge, an entirely inverted mechanism of substrate recognition that relies on the detection of single-stranded configurations in the undamaged complementary sequence of the double helix. PMID:17355181

Prenatal exposure to polycyclic aromatic hydrocarbons/aromatics, BDNF and child development

DOE Office of Scientific and Technical Information (OSTI.GOV)

Perera, Frederica, E-mail: fpp1@columbia.edu; Columbia Center for Children's Environmental Health, Columbia University, 722 W. 168th St., New York, NY 10032; Phillips, David H.

Objectives: Within a New York City (NYC) birth cohort, we assessed the associations between polycyclic aromatic hydrocarbon (PAH) and other aromatic DNA adducts and brain derived neurotrophic factor (BDNF) concentrations in umbilical cord blood, and neurodevelopment at age 2 years and whether BDNF is a mediator of the associations between PAH/aromatic-DNA adducts and neurodevelopment. Methods: PAH/aromatic-DNA adduct concentrations in cord blood were measured in 505 children born to nonsmoking African-American and Dominican women residing in NYC, and a subset was assessed for neurodevelopment at 2 years using the Bayley Scales of Infant Development Mental Development Index (MDI). A spectrum ofmore » PAH/aromatic-DNA adducts was measured using the {sup 32}P-postlabeling assay; DNA adducts formed by benzo[a]pyrene (B[a]P), a representative PAH, were measured by High Performance Liquid Chromatography (HPLC)/fluorescence. BDNF mature protein in cord blood plasma was quantified by an ELISA. Multivariate regression analysis, adjusting for potential confounders, was conducted. Results: PAH/aromatic-DNA adduct concentration measured by postlabeling was inversely associated with BDNF concentration (p=0.02) and with MDI scores at 2 years (p=0.04). BDNF level was positively associated with MDI scores (p=0.003). Restricting to subjects having all three measures (PAH/aromatic-DNA adducts by postlabeling, MDI, and BDNF), results were similar but attenuated (p=0.13, p=0.05, p=0.01, respectively). Associations between B[a]P-DNA adducts and BDNF and B[a]P-DNA adducts and MDI at age 2 years were not significant. At age 3 years, the positive association of BDNF with MDI was not observed. Conclusions: The results at age 2 suggest that prenatal exposure to a spectrum of PAH/aromatic pollutants may adversely affect early neurodevelopment, in part by reducing BDNF levels during the fetal period. However, the same relationship was not seen at age 3. - Highlights: • Cord blood

DEGRADATION OF POLYNUCLEAR AROMATIC HYDROCARBONS UNDER BENCH-SCALE COMPOST CONDITIONS

EPA Science Inventory

The relationship between biomass growth and degradation of polynuclear aromatic hydrocarbons (PAHs) in soil, and subsequent toxicity reduction, was evaluated in 10 in-vessel, bench-scale compost units. Field soil was aquired from the Reilly Tar and Chemical Company Superfund site...

New naphthalene whole-cell bioreporter for measuring and assessing naphthalene in polycyclic aromatic hydrocarbons contaminated site.

PubMed

Sun, Yujiao; Zhao, Xiaohui; Zhang, Dayi; Ding, Aizhong; Chen, Cheng; Huang, Wei E; Zhang, Huichun

2017-11-01

A new naphthalene bioreporter was designed and constructed in this work. A new vector, pWH1274_Nah, was constructed by the Gibson isothermal assembly fused with a 9 kb naphthalene-degrading gene nahAD (nahAa nahAb nahAc nahAd nahB nahF nahC nahQ nahE nahD) and cloned into Acinetobacter ADPWH_lux as the host, capable of responding to salicylate (the central metabolite of naphthalene). The ADPWH_Nah bioreporter could effectively metabolize naphthalene and evaluate the naphthalene in natural water and soil samples. This whole-cell bioreporter did not respond to other polycyclic aromatic hydrocarbons (PAHs; pyrene, anthracene, and phenanthrene) and demonstrated a positive response in the presence of 0.01 μM naphthalene, showing high specificity and sensitivity. The bioluminescent response was quantitatively measured after a 4 h exposure to naphthalene, and the model simulation further proved the naphthalene metabolism dynamics and the salicylate-activation mechanisms. The ADPWH_Nah bioreporter also achieved a rapid evaluation of the naphthalene in the PAH-contaminated site after chemical spill accidents, showing high consistency with chemical analysis. The engineered Acinetobacter variant had significant advantages in rapid naphthalene detection in the laboratory and potential in situ detection. The state-of-the-art concept of cloning PAHs-degrading pathway in salicylate bioreporter hosts led to the construction and assembly of high-throughput PAH bioreporter array, capable of crude oil contamination assessment and risk management. Copyright © 2017 Elsevier Ltd. All rights reserved.

Aromatization of n-hexane over ZnO/H-ZSM-5 catalysts

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kanai, J.; Kawata, N.

The mechanism of transformation of n-hexane into aromatics over ZnO/H-ZSM-5 catalyst has been investigated. The yields of aromatics in the transformation of n-hexane over H-ZSM-5 are enhanced by mechanical mixing of ZnO as well as by ion exchange or impregnation of zinc cation. It is concluded that aromatization of n-hexane over ZnO/H-ZSM-5 is a bifunctional reaction, and that ZnO as well as H-ZSM-5 takes part both in the activation of n-hexane and in the aromatization of lower olefins. By contrasting the conversion of n-hexane with that of 1-hexane, it is found that aromatization of n-hexane over ZnO/H-ZSM-5 involves both themore » dehydrogenation of n-hexane into hexene and that of the oligomerized products into aromatics. It is proposed that ZnO catalyzes the dehydrogenation of n-hexane into hexene and of the oligomerized products into aromatics.« less

Increased concentrations of polycyclic aromatic hydrocarbons in Alpine streams during annual snowmelt: investigating effects of sampling method, site characteristics, and meteorology.

PubMed

Shahpoury, Pourya; Hageman, Kimberly J; Matthaei, Christoph D; Alumbaugh, Robert E; Cook, Michelle E

2014-10-07

Silicone passive samplers and macroinvertebrates were used to measure time-integrated concentrations of polycyclic aromatic hydrocarbons (PAHs) in alpine streams during annual snowmelt. The three sampling sites were located near a main highway in Arthur's Pass National Park in the Southern Alps of New Zealand. A similar set of PAH congeners, composed of 2-4 rings, were found in silicone passive samplers and macroinvertebrates. The background PAH concentrations were similar at all sites, implying that proximity to the highway did not affect concentrations. In passive samplers, an increase of PAH concentrations by up to seven times was observed during snowmelt. In macroinvertebrates, the concentration changes were moderate; however, macroinvertebrate sampling did not occur during the main pulse observed in the passive samplers. The extent of vegetation in the catchment appeared to affect the concentration patterns seen at the different stream sites. A strong correlation was found between PAH concentrations in passive samplers and the amount of rainfall in the study area, indicating that the washout of contaminants from snowpack by rainfall was an important process.

Inter-domain Synergism Is Required for Efficient Feeding of Cellulose Chain into Active Site of Cellobiohydrolase Cel7A*

PubMed Central

Kont, Riin; Kari, Jeppe; Borch, Kim; Westh, Peter; Väljamäe, Priit

2016-01-01

Structural polysaccharides like cellulose and chitin are abundant and their enzymatic degradation to soluble sugars is an important route in green chemistry. Processive glycoside hydrolases (GHs), like cellobiohydrolase Cel7A of Trichoderma reesei (TrCel7A) are key components of efficient enzyme systems. TrCel7A consists of a catalytic domain (CD) and a smaller carbohydrate-binding module (CBM) connected through the glycosylated linker peptide. A tunnel-shaped active site rests in the CD and contains 10 glucose unit binding sites. The active site of TrCel7A is lined with four Trp residues with two of them, Trp-40 and Trp-38, in the substrate binding sites near the tunnel entrance. Although addressed in numerous studies the elucidation of the role of CBM and active site aromatics has been obscured by a complex multistep mechanism of processive GHs. Here we studied the role of the CBM-linker and Trp-38 of TrCel7A with respect to binding affinity, on- and off-rates, processivity, and synergism with endoglucanase. The CBM-linker increased the on-rate and substrate affinity of the enzyme. The Trp-38 to Ala substitution resulted in increased off-rates and decreased processivity. The effect of the Trp-38 to Ala substitution on on-rates was strongly dependent on the presence of the CBM-linker. This compensation between CBM-linker and Trp-38 indicates synergism between CBM-linker and CD in feeding the cellulose chain into the active site. The inter-domain synergism was pre-requisite for the efficient degradation of cellulose in the presence of endoglucanase. PMID:27780868

Inter-domain Synergism Is Required for Efficient Feeding of Cellulose Chain into Active Site of Cellobiohydrolase Cel7A.

PubMed

Kont, Riin; Kari, Jeppe; Borch, Kim; Westh, Peter; Väljamäe, Priit

2016-12-09

Structural polysaccharides like cellulose and chitin are abundant and their enzymatic degradation to soluble sugars is an important route in green chemistry. Processive glycoside hydrolases (GHs), like cellobiohydrolase Cel7A of Trichoderma reesei (TrCel7A) are key components of efficient enzyme systems. TrCel7A consists of a catalytic domain (CD) and a smaller carbohydrate-binding module (CBM) connected through the glycosylated linker peptide. A tunnel-shaped active site rests in the CD and contains 10 glucose unit binding sites. The active site of TrCel7A is lined with four Trp residues with two of them, Trp-40 and Trp-38, in the substrate binding sites near the tunnel entrance. Although addressed in numerous studies the elucidation of the role of CBM and active site aromatics has been obscured by a complex multistep mechanism of processive GHs. Here we studied the role of the CBM-linker and Trp-38 of TrCel7A with respect to binding affinity, on- and off-rates, processivity, and synergism with endoglucanase. The CBM-linker increased the on-rate and substrate affinity of the enzyme. The Trp-38 to Ala substitution resulted in increased off-rates and decreased processivity. The effect of the Trp-38 to Ala substitution on on-rates was strongly dependent on the presence of the CBM-linker. This compensation between CBM-linker and Trp-38 indicates synergism between CBM-linker and CD in feeding the cellulose chain into the active site. The inter-domain synergism was pre-requisite for the efficient degradation of cellulose in the presence of endoglucanase. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Single base substitution causing the fragrant phenotype and development of a type-specific marker in aromatic coconut (Cocos nucifera).

PubMed

Vongvanrungruang, A; Mongkolsiriwatana, C; Boonkaew, T; Sawatdichaikul, O; Srikulnath, K; Peyachoknagul, S

2016-09-19

The fragrance gene, betaine aldehyde dehydrogenase 2 (Badh2), has been well studied in many plant species. The objectives of this study were to clone Badh2 and compare the sequences between aromatic and non-aromatic coconuts. The complete coding region was cloned from cDNA of both aromatic and non-aromatic coconuts. The nucleotide sequences were highly homologous to Badh2 genes of other plants. Badh2 consisted of a 1512-bp open reading frame encoding 503 amino acids. A single nucleotide difference between aromatic and non-aromatic coconuts resulted in the conversion of alanine (non-aromatic) to proline (aromatic) at position 442, which was the substrate binding site of BADH2. The ring side chain of proline could destabilize the structure leading to a non-functional enzyme. Badh2 genomic DNA was cloned from exon 1 to 4, and from exon 5 to 15 from the two coconut types, except for intron 4 that was very long. The intron sequences of the two coconut groups were highly homologous. No differences in Badh2 expression were found among the tissues of aromatic coconut or between aromatic and non-aromatic coconuts. The amino acid sequences of BADH2 from coconut and other plants were compared and the genetic relationship was analyzed using MEGA 7.0. The phylogenetic tree reconstructed by the Bayesian information criterion consisted of two distinct groups of monocots and dicots. Among the monocots, coconut (Cocos nucifera) and oil palm (Elaeis guineensis) were the most closely related species. A marker for coconut differentiation was developed from one-base substitution site and could be successfully used.

Aromatic Borozene

PubMed Central

2009-01-01

Based on our comprehensive theoretical investigation and known experimental results for small boron clusters, we predict the existence of a novel aromatic inorganic molecule, B12H6. This molecule, which we refer to as borozene, has remarkably similar properties to the well-known benzene. Borozene is planar, possesses a large first excitation energy, D3hsymmetry, and more importantly is aromatic. Furthermore, the calculated anisotropy of the magnetic susceptibility of borozene is three times larger in absolute value than for benzene. Finally, we show that borozene molecules may be fused together to give larger aromatic compounds with even larger anisotropic susceptibilities. PMID:20596438

Reduction of aromatic and heterocyclic aromatic N-hydroxylamines by human cytochrome P450 2S1.

PubMed

Wang, Kai; Guengerich, F Peter

2013-06-17

Many aromatic amines and heterocyclic aromatic amines (HAAs) are known carcinogens for animals, and there is also strong evidence of some in human cancer. The activation of these compounds, including some arylamine drugs, involves N-hydroxylation, usually by cytochrome P450 enzymes (P450) in Family 1 (1A2, 1A1, and 1B1). We previously demonstrated that the bioactivation product of the anticancer agent 2-(4-amino-3-methylphenyl)-5-fluorobenzothiazole (5F 203), an N-hydroxylamine, can be reduced by P450 2S1 to its amine precursor under anaerobic conditions and, to a lesser extent, under aerobic conditions [Wang, K., and Guengerich, F. P. (2012) Chem. Res. Toxicol. 25, 1740-1751]. In the study presented here, we tested the hypothesis that P450 2S1 is involved in the reductive biotransformation of known carcinogenic aromatic amines and HAAs. The N-hydroxylamines of 4-aminobiphenyl (4-ABP), 2-naphthylamine (2-NA), and 2-aminofluorene (2-AF) were synthesized and found to be reduced by P450 2S1 under both anaerobic and aerobic conditions. The formation of amines due to P450 2S1 reduction also occurred under aerobic conditions but was less apparent because the competitive disproportionation reactions (of the N-hydroxylamines) also yielded amines. Further, some nitroso and nitro derivatives of the arylamines could also be reduced by P450 2S1. None of the amines tested were oxidized by P450 2S1. These results suggest that P450 2S1 may be involved in the reductive detoxication of several of the activated products of carcinogenic aromatic amines and HAAs.

Reduction of Aromatic and Heterocyclic Aromatic N-Hydroxylamines by Human Cytochrome P450 2S1

PubMed Central

Wang, Kai; Guengerich, F. Peter

2013-01-01

Many aromatic amines and heterocyclic aromatic amines (HAAs) are known carcinogens for animals and there is also strong evidence for some in human cancer. The activation of these compounds, including some arylamine drugs, involves N-hydroxylation, usually by cytochrome P450 enzymes (P450) in Family 1 (1A2, 1A1, and 1B1). We previously demonstrated that the bioactivation product of the anti-cancer agent 2-(4-amino-3-methylphenyl)-5-fluorobenzothiazole (5F 203), an N-hydroxylamine, can be reduced by P450 2S1 to its amine precursor under anaerobic conditions and, to a lesser extent, under aerobic conditions (Wang, K., and Guengerich, F. P. (2012) Chem. Res. Toxicol. 25, 1740–1751). In the present study, we tested the hypothesis that P450 2S1 is involved in the reductive biotransformation of known carcinogenic aromatic amines and HAAs. The N-hydroxylamines of 4-aminobiphenyl (4-ABP), 2-naphthylamine (2-NA), and 2-aminofluorene (2-AF) were synthesized and found to be reduced by P450 2S1 under both anaerobic and aerobic conditions. The formation of amines due to P450 2S1 reduction also occurred under aerobic conditions but was less apparent because the competitive disproportionation reactions (of the N-hydroxylamines) also yielded amines. Further, some nitroso and nitro derivatives of the arylamines could also be reduced by P450 2S1. None of the amines tested were oxidized by P450 2S1. These results suggest that P450 2S1 may be involved in the reductive detoxication of several of the activated products of carcinogenic aromatic amines and HAAs. PMID:23682735

Distributions of polycyclic aromatic hydrocarbons and alkylated polycyclic aromatic hydrocarbons in Osaka Bay, Japan.

PubMed

Miki, Shizuho; Uno, Seiichi; Ito, Kazuki; Koyama, Jiro; Tanaka, Hiroyuki

2014-08-30

Contaminations in sediments by polycyclic aromatic hydrocarbons (PAHs) and alkylated PAHs were investigated at 44 sites in Osaka Bay, Japan. Concentrations of total PAHs and alkylated PAHs were in the range 6.40-7800 ng/g dry weights and 13.7-1700 ng/g dry weights, respectively. The PAH concentrations tended to be higher along the shoreline in the vicinities of big ports, industrialized areas, and densely populated regions such as the cities of Osaka and Kobe. The major sources appeared to be pyrogenic or both pyrogenic and petrogenic at most of the sites. PAH concentrations were remarkably high at a site near Kobe, where the concentrations of dibenzo(a,h)anthracene and benzo(g,h,i)perylene exceeded the effects-range-medium concentration and eight PAHs were above the corresponding effects-range-low concentrations. Those PAHs may have been derived from the great fire associated with the large earthquake in 1995. Copyright © 2014 Elsevier Ltd. All rights reserved.

Bond Length Equalization with molecular aromaticity-A new measurement of aromaticity.

PubMed

Shen, Chen-Fei; Liu, Zi-Zhong; Liu, Hong-Xia; Zhang, Hui-Qing

2018-05-08

A new method to measure the amount of aromaticity is presented through the process of Bond Length Equalization (BLE). Degree of Aromaticity (DOA), a two-dimensional intensive quantity including geometric and energetic factors, as a new measurement of aromaticity is proposed. The unique characteristic of DOA and the formation of DOA will be displayed. The calculation of the geometrical optimization, DOA, Nucleus Independent Chemical Shifts (NICS) and Ring Stretching Vibration Raman Spectroscopy Frequency (RSVRSF) for the aromatic ring molecules - G n H n m (G = C, Si, Ge, n = 3, 5-8, m = +1, -1, 0, +1, +2) were calculated using the method of Density Functional Theory (DFT). The correlation between radius angle and molecular energy is absolute quadratic in the process of BLE. As the increasing of the number of ring atoms, the value of DOA decreasing gradually, the aromaticity decreased gradually, which was a same conclusion as NICS and RSVRSF concluded. Copyright © 2018 Elsevier B.V. All rights reserved.

Temporal and spatial variations of polycyclic aromatic hydrocarbon concentrations around a coke oven plant.

PubMed

Stella, Anna; Piccardo, Maria Teresa; Pala, Mauro; Balducci, Daniele; Cipolla, Massimo; Ceppi, Marcello; Valerio, Federico

2012-09-01

From 1995 to 2004, in Genoa, Italy, daily concentrations of twelve polycyclic aromatic hydrocarbons (PAHs) were measured in particulate phase (PM10), around a coke oven plant in operation from the 1950s and closed in 2002. The study permitted to identify the coke oven as the main PAH source in Genoa, causing constant exceeding of benzo(a)pyrene (BaP) air quality target (1.0 ng/m3) in the urban area till 1,900 meters distance downwind the plant. For this reason the plant was closed. Distance and daily hours downwind the coke plant were the main sources of variability of toxic BaP equivalent (BaPeq) concentrations and equations that best fitted these variables were experimentally obtained. During full plant activity, annual average BaPeq concentrations, measured in the three sampling sites aligned downwind to the summer prevalent winds, were: 85 ng/m3 at 40 m (site 2, industrial area), 13.2 ng/m3 at 300 m (site 3, residential area) and 5.6 ng/m3 at 575 m (site 4, residential area). Soon after the coke oven's closure (February 2002) BaPeq concentrations (annual average) measured in residential area, decreased drastically: 0.2 ng/m3 at site 3, 0.4 ng/m3 at site 4. Comparing 1998 and 2003 data, BaPeq concentrations decreased 97.6% in site 3 and 92.8% in site 4. Samples collected at site 3, during the longest downwind conditions, provided a reliable PAH profile of fugitive coke oven emissions. This profile was significantly different from the PAH profile, contemporary found at site 5, near the traffic flow. This study demonstrates that risk assessment based only on distance of residences from a coke plant can be heavily inaccurate and confirmed that seasonal variability of BaPeq concentrations and high variability of fugitive emissions of PAHs during coke oven activities require at least one year of frequent and constant monitoring (10-15 samples each month). Around a coking plant, polycyclic aromatic hydrocarbons (PAHs), concentrations depend mainly on downwind hours

Structure and function of CYP108D1 from Novosphingobium aromaticivorans DSM12444: an aromatic hydrocarbon-binding P450 enzyme.

PubMed

Bell, Stephen G; Yang, Wen; Yorke, Jake A; Zhou, Weihong; Wang, Hui; Harmer, Jeffrey; Copley, Rachel; Zhang, Aili; Zhou, Ruimin; Bartlam, Mark; Rao, Zihe; Wong, Luet Lok

2012-03-01

CYP108D1 from Novosphingobium aromaticivorans DSM12444 binds a range of aromatic hydrocarbons such as phenanthrene, biphenyl and phenylcyclohexane. Its structure, which is reported here at 2.2 Å resolution, is closely related to that of CYP108A1 (P450terp), an α-terpineol-oxidizing enzyme. The compositions and structures of the active sites of these two enzymes are very similar; the most significant changes are the replacement of Glu77 and Thr103 in CYP108A1 by Thr79 and Val105 in CYP108D1. Other residue differences lead to a larger and more hydrophobic access channel in CYP108D1. These structural features are likely to account for the weaker α-terpineol binding by CYP108D1 and, when combined with the presence of three hydrophobic phenylalanine residues in the active site, promote the binding of aromatic hydrocarbons. The haem-proximal surface of CYP108D1 shows a different charge distribution and topology to those of CYP101D1, CYP101A1 and CYP108A1, including a pronounced kink in the proximal loop of CYP108D1, which may result in poor complementarity with the [2Fe-2S] ferredoxins Arx, putidaredoxin and terpredoxin that are the respective redox partners of these three P450 enzymes. The unexpectedly low reduction potential of phenylcyclohexane-bound CYP108D1 (-401 mV) may also contribute to the low activity observed with these ferredoxins. CYP108D1 appears to function as an aromatic hydrocarbon hydroxylase that requires a different electron-transfer cofactor protein.

Aromatic Medicinal Plants of the Lamiaceae Family from Uzbekistan: Ethnopharmacology, Essential Oils Composition, and Biological Activities

PubMed Central

Mamadalieva, Nilufar Z.; Akramov, Davlat Kh.; Ovidi, Elisa; Tiezzi, Antonio; Nahar, Lutfun; Azimova, Shahnoz S.; Sarker, Satyajit D.

2017-01-01

Plants of the Lamiaceae family are important ornamental, medicinal, and aromatic plants, many of which produce essential oils that are used in traditional and modern medicine, and in the food, cosmetics, and pharmaceutical industry. Various species of the genera Hyssopus, Leonurus, Mentha, Nepeta, Origanum, Perovskia, Phlomis, Salvia, Scutellaria, and Ziziphora are widespread throughout the world, are the most popular plants in Uzbek traditional remedies, and are often used for the treatment of wounds, gastritis, infections, dermatitis, bronchitis, and inflammation. Extensive studies of the chemical components of these plants have led to the identification of many compounds, as well as essentials oils, with medicinal and other commercial values. The purpose of this review is to provide a critical overview of the literature surrounding the traditional uses, ethnopharmacology, biological activities, and essential oils composition of aromatic plants of the family Lamiaceae, from the Uzbek flora. PMID:28930224

Engineering Aromatic-Aromatic Interactions To Nucleate Folding in Intrinsically Disordered Regions of Proteins.

PubMed

Balakrishnan, Swati; Sarma, Siddhartha P

2017-08-22

Aromatic interactions are an important force in protein folding as they combine the stability of a hydrophobic interaction with the selectivity of a hydrogen bond. Much of our understanding of aromatic interactions comes from "bioinformatics" based analyses of protein structures and from the contribution of these interactions to stabilizing secondary structure motifs in model peptides. In this study, the structural consequences of aromatic interactions on protein folding have been explored in engineered mutants of the molten globule protein apo-cytochrome b 5 . Structural changes from disorder to order due to aromatic interactions in two variants of the protein, viz., WF-cytb5 and FF-cytb5, result in significant long-range secondary and tertiary structure. The results show that 54 and 52% of the residues in WF-cytb5 and FF-cytb5, respectively, occupy ordered regions versus 26% in apo-cytochrome b 5 . The interactions between the aromatic groups are offset-stacked and edge-to-face for the Trp-Phe and Phe-Phe mutants, respectively. Urea denaturation studies indicate that both mutants have a C m higher than that of apo-cytochrome b 5 and are more stable to chaotropic agents than apo-cytochrome b 5 . The introduction of these aromatic residues also results in "trimer" interactions with existing aromatic groups, reaffirming the selectivity of the aromatic interactions. These studies provide insights into the aromatic interactions that drive disorder-to-order transitions in intrinsically disordered regions of proteins and will aid in de novo protein design beyond small peptide scaffolds.

Evaluating porewater polycyclic aromatic hydrocarbon-related toxicity at a contaminated sediment site using a spiked field-sediment approach.

PubMed

Hartzell, Sharon E; Unger, Michael A; Vadas, George G; Yonkos, Lance T

2018-03-01

Although the complexity of contaminant mixtures in sediments can confound the identification of causative agents of adverse biological response, understanding the contaminant(s) of primary concern at impacted sites is critical to sound environmental management and remediation. In the present study, a stock mixture of 18 polycyclic aromatic hydrocarbon (PAH) compounds was prepared to reflect the variety and relative proportions of PAHs measured in surface sediment samples collected from discrete areas of a historically contaminated industrial estuary. This site-specific PAH stock mixture was spiked into nontoxic in-system and out-of-system field-collected reference sediments in dilution series spanning the range of previously measured total PAH concentrations from the region. Spiked sediments were evaluated in 10-d Leptocheirus plumulosus tests to determine whether toxicity in laboratory-created PAH concentrations was similar to the toxicity found in field-collected samples with equivalent PAH concentrations. The results show that toxicity of contaminated sediments was not explained by PAH exposure, while indicating that toxicity in spiked in-system (fine grain, high total organic carbon [TOC]) and out-of-system (course grain, low TOC) sediments was better explained by porewater PAH concentrations, measured using an antibody-based biosensor that quantified 3- to 5-ring PAHs, than total sediment PAH concentrations. The study demonstrates the application of site-specific spiking experiments to evaluate sediment toxicity at sites with complex mixtures of multiple contaminant classes and the utility of the PAH biosensor for rapid sediment-independent porewater PAH analysis. Environ Toxicol Chem 2018;37:893-902. © 2017 SETAC. © 2017 SETAC.

Comparison of carbon-sulfur and carbon-amine bond in therapeutic drug: 4β-S-aromatic heterocyclic podophyllum derivatives display antitumor activity

PubMed Central

Li, Jian-Long; Zhao, Wei; Zhou, Chen; Zhang, Ya-Xuan; Li, Hong-Mei; Tang, Ya-Ling; Liang, Xin-Hua; Chen, Tao; Tang, Ya-Jie

2015-01-01

Herein is a first effort to systematically study the significance of carbon-sulfur (C-S) and carbon-amine (C-NH) bonds on the antitumor proliferation activity of podophyllum derivatives and their precise mechanism of apoptosis. Compared with the derivative modified by a C-NH bond, the derivative modified by a C-S bond exhibited superior antitumor activity, the inhibition activity of target proteins tubulin or Topo II, cell cycle arrest, and apoptosis induction. Antitumor mechanistic studies showed that the death receptor and the mitochondrial apoptotic pathways were simultaneously activated by the C-S bond modified aromatic heterocyclic podophyllum derivatives with a higher cellular uptake percentage of 60–90% and induction of a higher level of reactive oxygen species (ROS). Only the mitochondrial apoptotic pathway was activated by the C-NH bond modified aromatic heterocyclic podophyllum derivatives, with a lower cellular uptake percentage of 40–50%. This study provided insight into effects of the C-S and C-NH bond modification on the improvement of the antitumor activity of Podophyllum derivatives. PMID:26443888

Bio-Based Aromatic Epoxy Monomers for Thermoset Materials.

PubMed

Ng, Feifei; Couture, Guillaume; Philippe, Coralie; Boutevin, Bernard; Caillol, Sylvain

2017-01-18

The synthesis of polymers from renewable resources is a burning issue that is actively investigated. Polyepoxide networks constitute a major class of thermosetting polymers and are extensively used as coatings, electronic materials, adhesives. Owing to their outstanding mechanical and electrical properties, chemical resistance, adhesion, and minimal shrinkage after curing, they are used in structural applications as well. Most of these thermosets are industrially manufactured from bisphenol A (BPA), a substance that was initially synthesized as a chemical estrogen. The awareness on BPA toxicity combined with the limited availability and volatile cost of fossil resources and the non-recyclability of thermosets implies necessary changes in the field of epoxy networks. Thus, substitution of BPA has witnessed an increasing number of studies both from the academic and industrial sides. This review proposes to give an overview of the reported aromatic multifunctional epoxide building blocks synthesized from biomass or from molecules that could be obtained from transformed biomass. After a reminder of the main glycidylation routes and mechanisms and the recent knowledge on BPA toxicity and legal issues, this review will provide a brief description of the main natural sources of aromatic molecules. The different epoxy prepolymers will then be organized from simple, mono-aromatic di-epoxy, to mono-aromatic poly-epoxy, to di-aromatic di-epoxy compounds, and finally to derivatives possessing numerous aromatic rings and epoxy groups.

Normal Modes Expose Active Sites in Enzymes.

PubMed

Glantz-Gashai, Yitav; Meirson, Tomer; Samson, Abraham O

2016-12-01

Accurate prediction of active sites is an important tool in bioinformatics. Here we present an improved structure based technique to expose active sites that is based on large changes of solvent accessibility accompanying normal mode dynamics. The technique which detects EXPOsure of active SITes through normal modEs is named EXPOSITE. The technique is trained using a small 133 enzyme dataset and tested using a large 845 enzyme dataset, both with known active site residues. EXPOSITE is also tested in a benchmark protein ligand dataset (PLD) comprising 48 proteins with and without bound ligands. EXPOSITE is shown to successfully locate the active site in most instances, and is found to be more accurate than other structure-based techniques. Interestingly, in several instances, the active site does not correspond to the largest pocket. EXPOSITE is advantageous due to its high precision and paves the way for structure based prediction of active site in enzymes.

Normal Modes Expose Active Sites in Enzymes

PubMed Central

Glantz-Gashai, Yitav; Samson, Abraham O.

2016-01-01

Accurate prediction of active sites is an important tool in bioinformatics. Here we present an improved structure based technique to expose active sites that is based on large changes of solvent accessibility accompanying normal mode dynamics. The technique which detects EXPOsure of active SITes through normal modEs is named EXPOSITE. The technique is trained using a small 133 enzyme dataset and tested using a large 845 enzyme dataset, both with known active site residues. EXPOSITE is also tested in a benchmark protein ligand dataset (PLD) comprising 48 proteins with and without bound ligands. EXPOSITE is shown to successfully locate the active site in most instances, and is found to be more accurate than other structure-based techniques. Interestingly, in several instances, the active site does not correspond to the largest pocket. EXPOSITE is advantageous due to its high precision and paves the way for structure based prediction of active site in enzymes. PMID:28002427

Sulfated Low Molecular Weight Lignins, Allosteric Inhibitors of Coagulation Proteinases via the Heparin Binding Site, Significantly Alter the Active Site of Thrombin and Factor Xa Compared to Heparin

PubMed Central

Henry, Brian L.; Desai, Umesh R.

2014-01-01

Sulfated low molecular weight lignins (LMWLs) have been found to bind in the heparin binding sites of coagulation proteinases. LMWLs represent a library of diverse non-carbohydrate, aromatic molecules which are structures different from heparin, but still potently inhibit thrombin and factor Xa. To better understand their mechanism of action, we studied the effects of three sulfated LMWLs (CDSO3, FDSO3, and SDSO3) on the active sites of thrombin and factor Xa. LMWLs were found to uniformly inhibit the catalytic activity of thrombin and factor Xa, regardless of the substrate used. Michaelis-Menten kinetic studies indicate that maximal velocity of hydrolysis of each chromogenic substrate decreases significantly in the presence of sulfated LMWLs, while the effect on Michaelis constant is dependent on the nature of the substrate. These studies indicate that LMWLs inhibit thrombin and factor Xa through allosteric disruption of the catalytic apparatus, specifically through the catalytic step. As opposed to heparin, LMWLs significantly alter the binding of the active site fluorescent ligand p-aminobenzamidine. LMWLs also had a greater effect on the molecular orientation of fluorescein-labeled His 57 than heparin. The molecular geometry surrounding the most important catalytic amino acid, Ser 195, was significantly altered by the binding of LMWLs while heparin had no measurable effect on Ser 195. These results further advance the concept of sulfated LMWLs as heparin mimics and will aid the design of anticoagulants based on their novel scaffold. PMID:25242245

Sulfated low molecular weight lignins, allosteric inhibitors of coagulation proteinases via the heparin binding site, significantly alter the active site of thrombin and factor xa compared to heparin.

PubMed

Henry, Brian L; Desai, Umesh R

2014-11-01

Sulfated low molecular weight lignins (LMWLs) have been found to bind in the heparin binding sites of coagulation proteinases. LMWLs represent a library of diverse non-carbohydrate, aromatic molecules which are structures different from heparin, but still potently inhibit thrombin and factor Xa. To better understand their mechanism of action, we studied the effects of three sulfated LMWLs (CDSO3, FDSO3, and SDSO3) on the active sites of thrombin and factor Xa. LMWLs were found to uniformly inhibit the catalytic activity of thrombin and factor Xa, regardless of the substrate used. Michaelis-Menten kinetic studies indicate that maximal velocity of hydrolysis of each chromogenic substrate decreases significantly in the presence of sulfated LMWLs, while the effect on Michaelis constant is dependent on the nature of the substrate. These studies indicate that LMWLs inhibit thrombin and factor Xa through allosteric disruption of the catalytic apparatus, specifically through the catalytic step. As opposed to heparin, LMWLs significantly alter the binding of the active site fluorescent ligand p-aminobenzamidine. LMWLs also had a greater effect on the molecular orientation of fluorescein-labeled His 57 than heparin. The molecular geometry surrounding the most important catalytic amino acid, Ser 195, was significantly altered by the binding of LMWLs while heparin had no measurable effect on Ser 195. These results further advance the concept of sulfated LMWLs as heparin mimics and will aid the design of anticoagulants based on their novel scaffold. Copyright © 2014 Elsevier Ltd. All rights reserved.

Polyphenylquinoxalines Via Aromatic Nucleophilic Displacement

NASA Technical Reports Server (NTRS)

Hergenrother, Paul M.; Connell, John W.

1991-01-01

Process for synthesis of polyphenylquinoxalines (PPQ's) involves nucleophilic displacement reactions of di(hydroxyphenyl) quinoxaline monomers with activated aromatic dihalides. New process costs less than other processes for synthesis of PPQ's. Facilitates synthesis of PPQ's of new and varied molecular structures. Useful as adhesives, coatings, films, membranes, and matrices for composites.

Design of aromatic-containing cell-penetrating peptide mimics with structurally modified π electronics.

PubMed

deRonde, Brittany M; Birke, Alexander; Tew, Gregory N

2015-02-09

Cell-penetrating peptides (CPPs) and their synthetic mimics (CPPMs) represent a class of molecules that facilitate the intracellular delivery of various cargo. Previous studies indicated that the presence of aromatic functionalities improved CPPM activity. Given that aromatic functionalities play prominent roles in membrane biology and participate in various π interactions, we explored whether these interactions could be optimized for improved CPPM activity. CPPMs were synthesized by ring-opening metathesis polymerization by using monomers that contained aromatic rings substituted with electron-donating and electron-withdrawing groups and covered an electrostatic potential range from -29.69 to +15.57 kcal mol(-1) . These groups altered the quadrupole moments of the aromatic systems and were used to test if such structural modifications changed CPPM activity. CPPMs were added to dye-loaded vesicles and the release of carboxyfluorescein was monitored as a function of polymer concentration. Changes in the effective polymer concentration to release 50% of the dye (effective concentration, EC50 ) were monitored. Results from this assay showed that the strength of the electron-donating and electron-withdrawing groups incorporated in the CPPMs did not alter polymer EC50 values or activity. This suggests that other design parameters may have a stronger impact on CPPM activity. In addition, these results indicate that a wide range of aromatic groups can be incorporated without negatively impacting polymer activity. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Health risks of polycyclic aromatic hydrocarbons via fish consumption in Haimen bay (China), downstream of an e-waste recycling site (Guiyu).

PubMed

Shi, Jingchun; Zheng, Gene Jin-Shu; Wong, Ming-Hung; Liang, Hong; Li, Yuelin; Wu, Yinglin; Li, Ping; Liu, Wenhua

2016-05-01

Guiyu, China has been one of the largest e-waste recycling sites of the world for more than 20 years. Abundant data show that local dwellers there suffered from severe health risks from e-waste contaminants. In this study, polycyclic aromatic hydrocarbons (PAHs) were used as candidates to test the contamination levels and their possible adverse effects on residents in Haimen Bay, the estuary of Lian River (less than 30km from Guiyu), which has been totally neglected. The concentrations of 16PAHs were determined in collected marine fish with a median ΣPAH concentration of 1478ng/g (wet weight), and the contamination may be mainly influenced by Lian River runoff, specifically from Guiyu. The lifetime excess cancer risk for local dwellers was much higher than the serious risk level (10(-4)). More seriously, outflows of PAHs from the e-waste recycling site (Guiyu) seemed to exert health risks of a much larger scale of population downstream. Copyright © 2016 Elsevier Inc. All rights reserved.

An ethnopharmacological study of aromatic Uyghur medicinal plants in Xinjiang, China.

PubMed

Zhao, Lu; Tian, Shuge; Wen, E; Upur, Halmuart

2017-12-01

An ethnobotanical survey was completed in a remote village and surrounding country of Xinjiang, where most Uyghur medicinal plants could be collected. This work clarifies and increases ethnobotanical data. We surveyed and organized aromatic medicinal plants that are commonly used in clinical settings to provide a significant reference for studying new medical activities. In the survey, informants who have traditional knowledge on aromatic Uyghur medicinal plants were interviewed between March 2014 and September 2014. Aromatic medicinal plant species and pertinent information were collected. Some therapeutic methods and modes of preparation of traditional aromatic medicinal plants were found. A total of 86 aromatic medicinal plant species belonging to 36 families were included in our study. We identified 34 plant species introduced from different regions such as Europe, India and Mediterranean areas. Fruits and whole plants were the most commonly used parts of plant, and most aromatic medicinal plants could be applied as medicine and food. We assigned the medicinal plants a use value (UV). Knowing the UV of species is useful in determining the use reliability and pharmacological features of related plants. Xinjiang is an area in which indigenous aromatic medicinal plants are diversely used and has therefore established a sound dimensional medical healthcare treatment system. Some aromatic Uyghur medicinal plants are on the verge of extinction. Hence, further strategies for the conservation of these aromatic medicinal plants should be prioritized.

Comparative study of n-hexane aromatization on Pt/KL, Pt/Mg(Al)O, and Pt/SiO{sub 2} catalysts: Clean and sulfur-containing feeds

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jacobs, G.; Padro, C.L.; Resasco, D.E.

The n-hexane aromatization has been studied on Pt/KL, Pt/Mg(Al)O, and Pt/SiO{sub 2} catalysts at 773 K using sulfur-free and 0.6 ppm sulfur containing feedstocks. Examination of the product distribution as a function of conversion suggests that the formation of benzene is preceded by the formation of hexenes. In contrast with previous reports, it has been found that the Pt/KL catalyst exhibits much higher aromatization activity than the Pt/Mg(Al)O catalyst. On Pt/KL the main product is benzene, with hexenes and lighter compounds as the principal by-products. By contrast, on the Pt/Mg(Al)O, the main products were hexenes. Since hexenes are primary productsmore » and benzene is a secondary product, the exceptional aromatization activity of Pt/KL is explained in terms of its ability to convert hexene into benzene. In the presence of sulfur, the Pt/KL exhibits a rapid loss in n-hexane conversion and benzene selectivity. Under these conditions, the sulfided Pt/KL catalyst presents a catalytic behavior typical of Pt/Mg(Al)O and Pt/SiO{sub 2}, generating larger amounts of hexenes. The observed results are consistent with the hypothesis that the most important role of the zeolite is to inhibit bimolecular interactions that lead to coke formation. The formation of coke has the net effect of selectively deactivating aromatization sites which require a large ensemble of atoms to constitute the active site but not affecting the dehydrogenation activity which is less ensemble-sensitive. Therefore, those particles that are not protected against coking inside the channels of the zeolite rapidly become unselective. In support of this hypothesis, the hydrogenolysis reaction which also requires a large ensemble of atoms, decreases in parallel with the aromatization reaction. The high sensitivity of Pt/KL to sulfur may be due to a combination of effects which may involve growth of metal particles outside the zeolite which would become unselective and partial poisoning of the

Cu-catalyzed C(sp³)-H bond activation reaction for direct preparation of cycloallyl esters from cycloalkanes and aromatic aldehydes.

PubMed

Zhao, Jincan; Fang, Hong; Han, Jianlin; Pan, Yi

2014-05-02

Cu-catalyzed dehydrogenation-olefination and esterification of C(sp(3))-H bonds of cycloalkanes with TBHP as an oxidant has been developed. The reaction involves four C-H bond activations and gives cycloallyl ester products directly from cycloalkanes and aromatic aldehydes.

Mycelia promote active transport and spatial dispersion of polycyclic aromatic hydrocarbons.

PubMed

Furuno, Shoko; Foss, Susan; Wild, Ed; Jones, Kevin C; Semple, Kirk T; Harms, Hauke; Wick, Lukas Y

2012-05-15

To cope with heterogeneous subsurface environments mycelial microorganisms have developed a unique ramified growth form. By extending hyphae, they can obtain nutrients from remote places and transport them even through air gaps and in small pore spaces, repectively. To date, studies have been focusing on the role that networks play in the distribution of nutrients. Here, we investigated the role of mycelia for the translocation of nonessential substances, using polycyclic aromatic hydrocarbons (PAHs) as model compounds. We show that the hyphae of the mycelial soil oomycete Pythium ultimum function as active translocation vectors for a wide range of PAHs. Visualization by two-photon excitation microscopy (TPEM) demonstrated the uptake and accumulation of phenanthrene (PHE) in lipid vesicles and its active transport by cytoplasmic streaming of the hyphae ('hyphal pipelines'). In mycelial networks, contaminants were translocated over larger distances than by diffusion. Given their transport capacity and ubiquity, hyphae may substantially distribute remote hydrophobic contaminants in soil, thereby improving their bioavailability to bacterial degradation. Hyphal contaminant dispersal may provide an untapped potential for future bioremediation approaches.

Deuterium enrichment of polycyclic aromatic hydrocarbons by photochemically induced exchange with deuterium-rich cosmic ices

NASA Technical Reports Server (NTRS)

Sandford, S. A.; Bernstein, M. P.; Allamandola, L. J.; Gillette, J. S.; Zare, R. N.

2000-01-01

The polycyclic aromatic hydrocarbon (PAH) coronene (C24H12) frozen in D2O ice in a ratio of less than 1 part in 500 rapidly exchanges its hydrogen atoms with the deuterium in the ice at interstellar temperatures and pressures when exposed to ultraviolet radiation. Exchange occurs via three different chemical processes: D atom addition, D atom exchange at oxidized edge sites, and D atom exchange at aromatic edge sites. Observed exchange rates for coronene (C24H12)-D2O and d12-coronene (C24D12)-H2O isotopic substitution experiments show that PAHs in interstellar ices could easily attain the D/H levels observed in meteorites. These results may have important consequences for the abundance of deuterium observed in aromatic materials in the interstellar medium and in meteorites. These exchange mechanisms produce deuteration in characteristic molecular locations on the PAHs that may distinguish them from previously postulated processes for D enrichment of PAHs.

Temperature-dependent regioselectivity of nucleophilic aromatic photosubstitution. Evidence that activation energy controls reactivity.

PubMed

Wubbels, Gene G; Tamura, Ryo; Gannon, Emmett J

2013-05-17

Irradiation (λ > 330 nm) of 2-chloro-4-nitroanisole (1) at 25 °C in aqueous NaOH forms three substitution photoproducts: 2-methoxy-5-nitrophenol (2), 2-chloro-4-nitrophenol (3), and 3-chloro-4-methoxyphenol (4), in chemical yields of 69.2%, 14.3%, and 16.5%. The activation energies for the elementary steps from the triplet state at 25 °C were determined to be 1.8, 2.4, and 2.7 kcal/mol, respectively. The chemical yields of each of the three products were determined for exhaustive irradiations at 0, 35, and 70 °C. The variation with temperature of the experimental yields is reproduced almost exactly by the yields calculated with the Arrhenius equation. This indicates that activation energy is the fundamental property related to regioselectivity in nucleophilic aromatic photosubstitution of the S(N)2 Ar* type. The many methods proposed for predicting regioselectivity in reactions of this type have had limited success and have not been related to activation energy.

Isotopic exchange of hydrogen in aromatic amino acids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pshenichnikova, A.B.; Karnaukhova, E.N.; Mitsner, B.I.

The kinetics of the isotopic replacement of hydrogen in the aromatic amino acids L-tryptophan, L-tyrosine, and L-phenylalanine in solutions of deuterochloric and deuterosulfuric acids in deuterium oxide were investigated by PMR spectroscopy. The reactions were shown to be of first orders with respect both to the concentration of the substrate and to the activity of the deuterium ion. The isotopic effects of hydrogen and the values of the activation energy of H-D exchange in different positions of the aromatic ring in tryptophan and tyrosine were determined. The effect of properties of the medium on the rate of the isotopic exchangemore » of hydrogen is discussed. 17 refs., 2 figs., 2 tabs.« less

Aromatization of n-hexane by platinum-containing molecular sieves. 2. n-Hexane reactivity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mielczarski, E.; Suk Bong Hong; Davis, M.E.

Pt/KL, Pt/BaKL, Pt/KBaKL, Pt/NaY, Pt/CsNaY, Pt/NaFAU(C), Pt/hex, Pt/SSZ-24, Pt/silica, and Pt/carbon were tested as catalysts for the aromatization of n-hexane at 460-510 C and atmospheric total pressure in order to study the influence of Pt cluster size and support acidity/basicity, microstructure, and chemical composition on activity and selectivity. Analysis of the catalytic and NH{sub 3} temperature-programmed desorption results from Pt/KL, Pt/BaKL, and Pt/KBaKL reveals that the presence of any acidity increases hydrogenolysis at the expense of benzene production. In addition, no increase in aromatization selectivity is observed by the addition of base sites to a Pt/zeolite catalyst, confirming that aromatizationmore » of n-hexane over Pt clusters on nonacidic carriers is monofunctional. High selectivity to benzene over most of the zeolite samples demonstrates that support microstructure does not contribute directly to the aromatization selectivity over Pt catalysts. High selectivity to benzene is observed for a Pt/carbon catalyst suggesting that a zeolitic support is not necessary for good performance. In fact, similar reactivity is obtained from microporous (Pt/SSZ-24) and nonmicroporous (Pt/silica) silica supported platinum catalysts with similar H/Pt values. A clear trend of increasing benzene selectivity with decreasing Pt cluster size is found. These observations suggest that the exceptional reactivity of Pt/KL for the aromatization of n-hexane results from the lack of any acidity in the support and the ability of zeolite L to stabilize the formation of extremely small Pt clusters.« less

Aromaticity at the water-hydrocarbon core interface of the membrane

PubMed Central

Lizardi-Ortiz, José E.; Hyzinski-García, María C.; Fernández-Gerena, José L.; Osorio-Martínez, Karen M.; Velázquez-Rivera, Eric; Valle-Avilés, Félix L.; Lasalde-Dominicci, José A.

2011-01-01

Almost all lipid-exposed transmembrane domains of integral proteins contain aromatic residues flanking the hydrophobic segment of the domains. These residues generally reside close to the carbonyl region of the membrane, and several structural and functional roles have been associated to these residues. Although the roles and physicochemical reasons for aromatic preference have been extensively studied using model systems, few studies have been done in a native membrane system. To gain insight about the mechanistic implication for this aromatic preference, we selected position αF426 of the muscle-type nicotinic acetylcholine receptor (nAChR). αF426 is a lipid-exposed residue at the extracellular segment of the αM4 transmembrane domain and is highly conserved among different nAChR subunits and species. We used site-directed mutagenesis, α-Bungarotoxin-binding assay, and two-electrodes voltage clamp in Xenopus laevis oocytes to characterize mutations at position αF426, which impart different physicochemical properties like volume, polarity, hydrogen bonds, aromaticity and net electrical charge. All mutations except the aromatic residues resulted in a significant reduction of the nAChR cell-surface levels and the macroscopic currents to acetylcholine. These results suggest that position αF426 contributes to structural stability and open-close transitions of the nAChR. Finally, the present study also provides information about how intermolecular interactions at position α426 modulate open-close transitions of the nAChR. PMID:18836298

Enhanced intersystem crossing in core-twisted aromatics.

PubMed

Nagarajan, Kalaivanan; Mallia, Ajith R; Muraleedharan, Keerthi; Hariharan, Mahesh

2017-03-01

We describe the design, bottom-up synthesis and X-ray single crystal structure of systematically twisted aromatics 1c and 2d for efficient intersystem crossing. Steric congestion at the cove region creates a nonplanar geometry that induces a significant yield of triplet excited states in the electron-poor core-twisted aromatics 1c and 2d . A systematic increase in the number of twisted regions in 1c and 2d results in a concomitant enhancement in the rate and yield of intersystem crossing, monitored using femtosecond and nanosecond transient absorption spectroscopy. Time-resolved absorption spectroscopic measurements display enhanced triplet quantum yields ( Φ T = 10 ± 1% for 1c and Φ T = 30 ± 2% for 2d ) in the twisted aromatics when compared to a negligible Φ T (<1%) in the planar analog 3c . Twist-induced spin-orbit coupling via activated out-of-plane C-H/C 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000

Metallo-deuteroporphyrin as a biomimetic catalyst for the catalytic oxidation of lignin to aromatics.

PubMed

Zhu, Chenjie; Ding, Weiwei; Shen, Tao; Tang, Chenglun; Sun, Chenguo; Xu, Shichao; Chen, Yong; Wu, Jinglan; Ying, Hanjie

2015-05-22

A series of metallo-deuteroporphyrins derived from hemin were prepared as models of the cytochrome P450 enzyme. With the aid of the highly active Co(II) deuteroporphyrin complex, the catalytic oxidation system was applied for the oxidation of several lignin model compounds, and high yields of monomeric products were obtained under mild reaction conditions. It was found that the modified cobalt deuteroporphyrin that has no substituents at the meso sites but does have the disulfide linkage in the propionate side chains at the β sites exhibited much higher activity and stability than the synthetic tetraphenylporphyrin. The changes in the propionate side chains can divert the reactivity of cobalt deuteroporphyrins from the typical CC bond cleavage to CO bond cleavage. Furthermore, this novel oxidative system can convert enzymolysis lignin into depolymerized products including a significant portion of well-defined aromatic monomers. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

On the Extraction of Aromatic Compounds from Hydrocarbons by Imidazolium Ionic Liquids

PubMed Central

Cassol, Cláudia C.; Umpierre, Alexandre P.; Ebeling, Günter; Ferrera, Bauer; Chiaro, Sandra S. X.; Dupont, Jairton

2007-01-01

The liquid-liquid equilibrium for the ternary system formed by n-octane and aromatic (alkylbenzenes) and heteroaromatic compounds (nitrogen and sulfur containing heterocyles) and 1-alkyl-3-methylimidazolium ionic liquids (ILs) associated with various anions has been investigated. The selectivity on the extraction of a specific aromatic compound is influenced by anion volume, hydrogen bond strength between the anion and the imidazolium cation and the length of the 1-methyl-3-alkylimidazolium alkyl side chain. The interaction of alkylbenzenes and sulfur heterocyles with the IL is preferentially through CH-π hydrogen bonds and the quantity of these aromatics in the IL phase decreases with the increase of the steric hindrance imposed by the substituents on the aromatic nucleus. In the case of nitrogen heterocycles the interaction occurs preferentially through N(heteroaromatic)-H(imidazolium) hydrogen bonds and the extraction process is largely controlled by the nitrogen heterocycle pKa. Competitive extraction experiments suggest that benzene, pyridine and dibenzothiophene do not compete for the same hydrogen bond sites of the IL.

Influence of Cadmium and Mercury on Activities of Ligninolytic Enzymes and Degradation of Polycyclic Aromatic Hydrocarbons by Pleurotus ostreatus in Soil

PubMed Central

Baldrian, Petr; in der Wiesche, Carsten; Gabriel, Jiří; Nerud, František; Zadražil, František

2000-01-01

The white-rot fungus Pleurotus ostreatus was able to degrade the polycyclic aromatic hydrocarbons (PAHs) benzo[a]anthracene, chrysene, benzo[b]fluoranthene, benzo[k]fluoranthene, benzo[a]pyrene, dibenzo[a,h]anthracene, and benzo[ghi]perylene in nonsterile soil both in the presence and in the absence of cadmium and mercury. During 15 weeks of incubation, recovery of individual compounds was 16 to 69% in soil without additional metal. While soil microflora contributed mostly to degradation of pyrene (82%) and benzo[a]anthracene (41%), the fungus enhanced the disappearance of less-soluble polycyclic aromatic compounds containing five or six aromatic rings. Although the heavy metals in the soil affected the activity of ligninolytic enzymes produced by the fungus (laccase and Mn-dependent peroxidase), no decrease in PAH degradation was found in soil containing Cd or Hg at 10 to 100 ppm. In the presence of cadmium at 500 ppm in soil, degradation of PAHs by soil microflora was not affected whereas the contribution of fungus was negligible, probably due to the absence of Mn-dependent peroxidase activity. In the presence of Hg at 50 to 100 ppm or Cd at 100 to 500 ppm, the extent of soil colonization by the fungus was limited. PMID:10831426

Polybenzimidazoles Via Aromatic Nucleophilic Displacement

NASA Technical Reports Server (NTRS)

Connell, John W.; Hergenrother, Paul M.; Smith, Joseph G.

1994-01-01

Soluble polybenzimidazoles (PBI's) synthesized by nucleophilic displacement reaction of di(hydroxyphenyl)-benzimidazole monomers with activated aromatic difluoride compounds in presence of anhydrous potassium carbonate. These polymers exhibit good thermal, thermo-oxidative, and chemical stability, and high mechanical properties. Using benzimidazole monomers, more economical, and new PBI's processed more easily than commercial PBI, without loss of desirable physical properties.

Antioxidant activity of selenenamide-based mimic as a function of the aromatic thiols nucleophilicity, a DFT-SAPE model.

PubMed

Kheirabadi, Ramesh; Izadyar, Mohammad

2018-05-18

The mechanism of action of the selenenamide 1 as a mimic of the glutathione peroxidase (GPx) was investigated by the density functional theory. The solvent-assisted proton exchange procedure was applied to model the catalytic behavior and antioxidant activity of this mimic. To have an insight into the charge transfer effect, different aromatic thiols, including electron donating substituents on the phenyl ring were considered. The catalytic behavior of the selenenamide was modeled in a four-step mechanism, described by the oxidation of the mimic, the reduction of the obtained product, selenoxide, the reduction of the selenenylsulfide and dehydration of selenenic acid. On the basis of the activation parameters, the final step of the proposed mechanism is the rate determining states of the catalytic cycle. Turnover frequency (TOF) analysis showed that the electron donating groups at the para-position of the phenyl ring of the PhSH do not affect the catalytic activity of the selenenamide in contrast to p-methyl thiophenol which indicates the highest nucleophilicity. The evaluation of the electronic contribution of the various donating groups on the phenyl ring of the aromatic thiols shows that the antioxidant activity of the selenenamide sufficiently increases in the presence of the electron-donating substitutions. Finally, the charge transfer process at the rate-determining state was investigated based on the natural bond orbital analysis. Copyright © 2018 Elsevier Ltd. All rights reserved.

Heterocyclic Aromatics in Petroleum Coke, Snow, Lake Sediments, and Air Samples from the Athabasca Oil Sands Region.

PubMed

Manzano, Carlos A; Marvin, Chris; Muir, Derek; Harner, Tom; Martin, Jonathan; Zhang, Yifeng

2017-05-16

The aromatic fractions of snow, lake sediment, and air samples collected during 2011-2014 in the Athabasca oil sands region were analyzed using two-dimensional gas chromatography following a nontargeted approach. Commonly monitored aromatics (parent and alkylated-polycyclic aromatic hydrocarbons and dibenzothiophenes) were excluded from the analysis, focusing mainly on other heterocyclic aromatics. The unknowns detected were classified into isomeric groups and tentatively identified using mass spectral libraries. Relative concentrations of heterocyclic aromatics were estimated and were found to decrease with distance from a reference site near the center of the developments and with increasing depth of sediments. The same heterocyclic aromatics identified in snow, lake sediments, and air were observed in extracts of delayed petroleum coke, with similar distributions. This suggests that petroleum coke particles are a potential source of heterocyclic aromatics to the local environment, but other oil sands sources must also be considered. Although the signals of these heterocyclic aromatics diminished with distance, some were detected at large distances (>100 km) in snow and surface lake sediments, suggesting that the impact of industry can extend >50 km. The list of heterocyclic aromatics and the mass spectral library generated in this study can be used for future source apportionment studies.

Compactness Aromaticity of Atoms in Molecules

PubMed Central

Putz, Mihai V.

2010-01-01

A new aromaticity definition is advanced as the compactness formulation through the ratio between atoms-in-molecule and orbital molecular facets of the same chemical reactivity property around the pre- and post-bonding stabilization limit, respectively. Geometrical reactivity index of polarizability was assumed as providing the benchmark aromaticity scale, since due to its observable character; with this occasion new Hydrogenic polarizability quantum formula that recovers the exact value of 4.5 a03 for Hydrogen is provided, where a0 is the Bohr radius; a polarizability based–aromaticity scale enables the introduction of five referential aromatic rules (Aroma 1 to 5 Rules). With the help of these aromatic rules, the aromaticity scales based on energetic reactivity indices of electronegativity and chemical hardness were computed and analyzed within the major semi-empirical and ab initio quantum chemical methods. Results show that chemical hardness based-aromaticity is in better agreement with polarizability based-aromaticity than the electronegativity-based aromaticity scale, while the most favorable computational environment appears to be the quantum semi-empirical for the first and quantum ab initio for the last of them, respectively. PMID:20480020

Modulation of ethoxyresorufin O-deethylase and glutathione S-transferase activities in Nile tilapia (Oreochromis niloticus) by polycyclic aromatic hydrocarbons containing two to four rings: implications in biomonitoring aquatic pollution.

PubMed

Pathiratne, Asoka; Hemachandra, Chamini K

2010-08-01

Despite ubiquity of polycyclic aromatic hydrocarbons (PAHs) in the tropical environments, little information is available concerning responses of tropical fish to PAHs and associated toxicity. In the present study, effects of five PAHs containing two to four aromatic rings on hepatic CYP1A dependent ethoxyresorufin O-deethylase (EROD), glutathione S-transferase (GST) and serum sorbitol dehydrogenase (SDH) activities in Nile tilapia, a potential fish species for biomonitoring pollution in tropical waters, were evaluated. Results showed that EROD activities were induced by the PAHs containing four aromatic rings (pyrene and chrysene) in a dose dependent manner. However PAHs with two to three aromatic rings (naphthalene, phenanthrene and fluoranthene) caused no effect or inhibition of EROD activities depending on the dose and the duration. Fluoranthene was the most potent inhibitor. SDH results demonstrated that high doses of fluoranthene induced hepatic damage. GST activity was induced by the lowest dose of phenanthrene, fluoranthene and chrysene but high doses had no effect. The results indicate that induction of EROD enzyme in Nile tilapia is a useful biomarker of exposure to PAHs such as pyrene and chrysene. However EROD inhibiting PAHs such as fluoranthene in the natural environment may modulate the EROD inducing potential of other PAHs thereby influencing PAH exposure assessments.

Transformations of Aromatic Compounds by Nitrosomonas europaea

PubMed Central

Keener, William K.; Arp, Daniel J.

1994-01-01

Benzene and a variety of substituted benzenes inhibited ammonia oxidation by intact cells of Nitrosomonas europaea. In most cases, the inhibition was accompanied by transformation of the aromatic compound to a more oxidized product or products. All products detected were aromatic, and substituents were often oxidized but were not separated from the benzene ring. Most transformations were enhanced by (NH4)2SO4 (12.5 mM) and were prevented by C2H2, a mechanism-based inactivator of ammonia monooxygenase (AMO). AMO catalyzed alkyl substituent hydroxylations, styrene epoxidation, ethylbenzene desaturation to styrene, and aniline oxidation to nitrobenzene (and unidentified products). Alkyl substituents were preferred oxidation sites, but the ring was also oxidized to produce phenolic compounds from benzene, ethylbenzene, halobenzenes, phenol, and nitrobenzene. No carboxylic acids were identified. Ethylbenzene was oxidized via styrene to two products common also to oxidation of styrene; production of styrene is suggestive of an electron transfer mechanism for AMO. Iodobenzene and 1,2-dichlorobenzene were oxidized slowly to halophenols; 1,4-dichlorobenzene was not transformed. No 2-halophenols were detected as products. Several hydroxymethyl (-CH2OH)-substituted aromatics and p-cresol were oxidized by C2H2-treated cells to the corresponding aldehydes, benzaldehyde was reduced to benzyl alcohol, and o-cresol and 2,5-dimethylphenol were not depleted. PMID:16349282

Inhibition of hydroxyl radical reaction with aromatics by dissolved natural organic matter

USGS Publications Warehouse

Lindsey, M.E.; Tarr, M.A.

2000-01-01

Reaction of aromatic compounds with hydroxyl radical is inhibited by dissolved natural organic matter (NOM). The degree of inhibition is significantly greater than that expected based on a simple model in which aromatic compound molecules bound to NOM are considered to be unreactive. In this study, hydroxyl radical was produced at steady-state concentrations using Fenton chemistry (H2O2 + Fe2+ ??? Fe3+ + HO- + HO??). Suwannee River fulvic acid and humic acid were used as NOM. The most likely mechanism for the observed inhibition is that hydroxyl radical formation occurs in microenvironmental sites remote from the aromatic compounds. In addition to changes in kinetics, pyrene hydroxyl radical reaction also exhibited a mechanistic change in the presence of fulvic acid. The mechanism changed from a reaction that was apparently firstorder in pyrene to one that was apparently secondorder in pyrene, indicating that pyrene self-reaction may have become the dominant mechanism in the presence of fulvic acid. Dissolved NOM causes significant changes in the rate and mechanism of hydroxyl radical degradation of aromatic compounds. Consequently, literature rate constants measured in pure water will not be useful for predicting the degradation of pollutants in environmental systems. The kinetic and mechanistic information in this study will be useful for developing improved degradation methods involving Fenton chemistry.Reaction of aromatic compounds with hydroxyl radical is inhibited by dissolved natural organic matter (NOM). The degree of inhibition is significantly greater than that expected based on a simple model in which aromatic compounds molecules bounds to NOM are considered to be unreactive. In this study, hydroxyl radical was produced at steady-state concentrations using Fenton chemistry (H2O2 + Fe2+ ??? Fe3+ + HO- + HO??). Suwannee River fulvic acid and humic acid were used as NOM. The most likely mechanisms for the observed inhibition is that hydroxyl radical

PERFLUORINATED AROMATIC COMPOUND

DTIC Science & Technology

octafluorobiphenyl, and perfluoroaliphatic aldehydes. Synthetic routes to perfluoro cyclohexyls via reactions of phenyl and pentafluorphenyl lithium with...other perfluorinated aromatic compounds were employed in the synthesis of perfluorinated aromatic model compounds and polymers. The hydrogenic analogues...hydrazides, and imides. Synthetic routes to perfluoro aralkyl compounds are being investigated. Starting materials are tetrafluorobenzene

Polycyclic aromatic hydrocarbons pollution effect on soil biological activity in the anthropogenic contaminated area

NASA Astrophysics Data System (ADS)

Batukaev, Abdulmalik; Sushkova, Svetlana; Minkina, Tatiana; Antonenko, Elena; Salamova, Anzhelika; Gimp, Alina; Deryabkina, Irina

2017-04-01

Polycyclic aromatic hydrocarbons (PAHs) are one of the most significant environmental contaminants with mutagenic and carcinogenic properties to all living organisms. The changes in microbial community structure in technogenic polluted soil may be used as tools for predicting and monitoring natural degradation and for search the most effective and appropriate pathways of bioremediation. The present study is aimed to research the biological activity of the soil in the emission zone of Novocherkassk Power station (NPs) (Russia) polluted by PAHs in 2015. The NPs is one of the largest thermal power stations in the south of Russia burning low-quality coal appurtenant the enterprises of I hazardous class. Monitoring plots were located on virgin or no-till fallow areas and not subject to the sanitary-protection zone of the NPs. Soil samples were taken from a depth of 0- to 20-cm, because the major part of PAHs are accumulated in the surface soil layer. The soils of the plots mainly include Chernozems Calcic (plots 1, 4, 5, 7, 9 and 10), Phaeozems Haplic (plots 3, 6, 8 and 11) Fluvisols Umbric (plots 2 and 12). In the soil of 12 monitoring plots located around NPs there were determined the main enzymes, abundance of soil bacteria and 17 priority PAHs. PAHs extraction from soil was performed by new developed ecologically clean method of subcritical water extraction without organic solvents (Sushkova et al., 2015). The level of PAHs around NPs is high at the nearest to factory monitoring plots situated at distance 1,0-1,2 km and reaches from 1600,1±14,7 up to 373,6±7,1 mkg/kg in the 20-cm soil layer. Gradually decrease of PAHs contamination is observed while increasing the distance from the NPs. The level of highmolecular PAHs (4-6 aromatic rings) exceeds the level of lowmolecular (2-3 aromatic rings) PAHs in all monitoring plots situated though the prevailing wind direction from NPs. The close correlations were found between PAHs content and biological activity parameters

Fluorescence method for enzyme analysis which couples aromatic amines with aromatic aldehydes

DOEpatents

Smith, R.E.; Dolbeare, F.A.

1980-10-21

Analysis of proteinases is accomplished using conventional amino acid containing aromatic amine substrates. Aromatic amines such as 4-methoxy-2-naphthylamine (4M2NA), 2-naphthylamine, aminoisophthalic acid dimethyl ester, p-nitroaniline, 4-methoxy-1-aminofluorene and coumarin derivatives resulting from enzymatic hydrolysis of the substrate couples with aromatic aldehydes such as 5-nitrosalicylaldehyde (5-NSA), benzaldehyde and p-nitrobenzaldehyde to produce Schiff-base complexes which are water insoluble. Certain Schiff-base complexes produce a shift from blue to orange-red (visible) fluorescence. Such complexes are useful in the assay of enzymes. No Drawings

Fluorescence method for enzyme analysis which couples aromatic amines with aromatic aldehydes

DOEpatents

Smith, Robert E. [557 Escondido Cir., Livermore, CA 94550; Dolbeare, Frank A. [5178 Diane La., Livermore, CA 94550

1980-10-21

Analysis of proteinases is accomplished using conventional amino acid containing aromatic amine substrates. Aromatic amines such as 4-methoxy-2-naphthylamine (4M2NA), 2-naphthylamine, aminoisophthalic acid dimethyl ester, p-nitroaniline, 4-methoxy-1-aminofluorene and coumarin derivatives resulting from enzymatic hydrolysis of the substrate couples with aromatic aldehydes such as 5-nitrosalicylaldehyde (5-NSA), benzaldehyde and p-nitrobenzaldehyde to produce Schiff-base complexes which are water insoluble. Certain Schiff-base complexes produce a shift from blue to orange-red (visible) fluorescence. Such complexes are useful in the assay of enzymes.

Fluorescence method for enzyme analysis which couples aromatic amines with aromatic aldehydes

DOEpatents

Smith, Robert E.; Dolbeare, Frank A.

1979-01-01

Analysis of proteinases is accomplished using conventional amino acid containing aromatic amine substrates. Aromatic amines such as 4-methoxy-2-naphthylamine (4M2NA), 2-naphthylamine, aminoisophthalic acid dimethyl ester, p-nitroaniline, 5-methoxy-1-aminofluorene and coumarin derivatives resulting from enzymatic hydrolysis of the substrate couples with aromatic aldehydes such as 5-nitrosalicylaldehyde (5-NSA), benzaldehyde and p-nitrobenzaldehyde to produce Schiff-base complexes which are water insoluble. Certain Schiff-base complexes produce a shift from blue to orange-red (visible) fluorescence. Such complexes are useful in the assay of enzymes.

Atmospheric behaviors of polycyclic aromatic hydrocarbons at a Japanese remote background site, Noto peninsula, from 2004 to 2014

NASA Astrophysics Data System (ADS)

Tang, Ning; Hakamata, Mariko; Sato, Kousuke; Okada, Yumi; Yang, Xiaoyang; Tatematsu, Michiya; Toriba, Akira; Kameda, Takayuki; Hayakawa, Kazuichi

2015-11-01

Total suspended particulates were collected at a Japanese remote background site (Noto Air Monitoring Station; NAMS) on the Noto Peninsula from September 2004 to June 2014. Nine polycyclic aromatic hydrocarbons (PAHs) in the particulates (fluoranthene, pyrene, benz[a]anthracene, chrysene, benzo[b]fluoranthene, benzo[k]fluoranthene, benzo[a]pyrene, benzo[ghi]perylene and indeno[1,2,3-cd]pyrene) were determined by HPLC with fluorescence detection. The mean total concentrations of the nine PAHs in the cold season (November to May for the years 2004-2014) was 670 pg m-3 (range 37-4100 pg m-3). The mean total concentration in the warm season (June to October for the same period) was 170 pg m-3 (range 31-960 pg m-3). The atmospheric PAH level at NAMS decreased in recent years, although no significant change was found in the warm season. An analysis of meteorological conditions showed that the atmospheric PAHs at NAMS were long range transported from Northeast China in the cold seasons and were contributed to by Japanese domestic sources in the warm seasons. Lower concentration ratios of reactive PAHs to their isomers at NAMS also supported these results. Activities associated with the Beijing Olympic and Paralympic Games in 2008 and reconstruction after the 2007 Noto Hanto earthquake may have contributed to the yearly variations of atmospheric PAH levels at NAMS during the period 2007-2009. Source control measures implemented by the Chinese and Japanese governments appear to have been effective in decreasing the atmospheric PAH levels at NAMS in recent years.

Discovering Chemical Aromaticity Using Fragrant Plants

ERIC Educational Resources Information Center

Schneider, Tanya L.

2010-01-01

Introductory organic chemistry is often perceived as inaccessible by students. This article describes a method used to link organic chemistry to everyday experience, asking students to explore whether fragrant molecules are also aromatic in the chemical sense. Students were engaged in this activity, excited about their results, and performed well…

Biodegradation of aliphatic vs. aromatic hydrocarbons in fertilized arctic soils

USGS Publications Warehouse

Braddock, J.F.

1999-01-01

A study was carried out to test a simple bioremediation treatment strategy in the Arctic and analyze the influence of fertilization the degradation of aliphatic and aromatic hydrocarbons, e.g., pristine, n-tetradecane, n-pentadecane, 2-methylnaphthalene, naphthalene, and acenaphthalene. The site was a coarse sand pad that once supported fuel storage tanks. Diesel-range organics concentrations were 250-860 mg/kg soil at the beginning of the study. Replicate field plots treated with fertilizer yielded final concentrations of 0, 50, 100, or 200 mg N/kg soil. Soil pH and soil-water potentials decreased due to fertilizer application. The addition of fertilizer considerably increased soil respiration potentials, but not the populations of microorganisms measured. Fertilizer addition also led to ??? 50% loss of measured aliphatic and aromatic hydrocarbons in surface and subsurface soils. For fertilized plots, hydrocarbon loss was not associated with the quantity of fertilizer added. Losses of aliphatic hydrocarbons were ascribed to biotic processes, while losses of aromatic hydrocarbons were due to biotic and abiotic processes.

Gas-phase reactions of phenyl radicals with aromatic molecules

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fahr, A.; Stein, S.E.

1988-08-25

Relative rates of reactions of phenyl radicals with a series of aromatic and polycyclic aromatic compounds are reported. Most studies were done in static reactors at 450/degrees/C using diphenyl diketone (benzil) as the phenyl radical source. Reactions with the following molecules are reported: benzene, toluene, p-xylene, 1,3,5-trimethylbenzene, phenol, bromobenzene, naphthalene, biphenyl, anthracene, 9-methylanthracene, and triphenylene. For reactions with substituted benzenes, H abstraction is the dominant reaction. Relative rates of phenylation at different sites do not closely follow established trends for rates of radical attack. It is proposed that these deviations are primarily due to a dependence of the degree ofmore » reversibility on the specific site of phenylation. These studies also show that the rates of phenyl and H-atom migration around the ring in adduct radicals are slow relative to dissociation. Also, by use of these results to link literature rate data from high and low temperatures, a rate expression for H abstraction from p-xylene by phenyl of 10/sup 9.6/ exp(-4.4 kcal/RT) M/sup /minus/1/ s/sup /minus/1/ is derived.« less

Aromatic metabolism of filamentous fungi in relation to the presence of aromatic compounds in plant biomass.

PubMed

Mäkelä, Miia R; Marinović, Mila; Nousiainen, Paula; Liwanag, April J M; Benoit, Isabelle; Sipilä, Jussi; Hatakka, Annele; de Vries, Ronald P; Hildén, Kristiina S

2015-01-01

The biological conversion of plant lignocellulose plays an essential role not only in carbon cycling in terrestrial ecosystems but also is an important part of the production of second generation biofuels and biochemicals. The presence of the recalcitrant aromatic polymer lignin is one of the major obstacles in the biofuel/biochemical production process and therefore microbial degradation of lignin is receiving a great deal of attention. Fungi are the main degraders of plant biomass, and in particular the basidiomycete white rot fungi are of major importance in converting plant aromatics due to their ability to degrade lignin. However, the aromatic monomers that are released from lignin and other aromatic compounds of plant biomass are toxic for most fungi already at low levels, and therefore conversion of these compounds to less toxic metabolites is essential for fungi. Although the release of aromatic compounds from plant biomass by fungi has been studied extensively, relatively little attention has been given to the metabolic pathways that convert the resulting aromatic monomers. In this review we provide an overview of the aromatic components of plant biomass, and their release and conversion by fungi. Finally, we will summarize the applications of fungal systems related to plant aromatics. Copyright © 2015 Elsevier Inc. All rights reserved.

Selectivity Control in the Tandem Aromatization of Bio‐Based Furanics Catalyzed by Solid Acids and Palladium

PubMed Central

Genuino, Homer C.; Thiyagarajan, Shanmugam; van der Waal, Jan C.; van Haveren, Jacco; Weckhuysen, Bert M.

2016-01-01

Abstract Bio‐based furanics can be aromatized efficiently by sequential Diels–Alder (DA) addition and hydrogenation steps followed by tandem catalytic aromatization. With a combination of zeolite H‐Y and Pd/C, the hydrogenated DA adduct of 2‐methylfuran and maleic anhydride can thus be aromatized in the liquid phase and, to a certain extent, decarboxylated to give high yields of the aromatic products 3‐methylphthalic anhydride and o‐ and m‐toluic acid. Here, it is shown that a variation in the acidity and textural properties of the solid acid as well as bifunctionality offers a handle on selectivity toward aromatic products. The zeolite component was found to dominate selectivity. Indeed, a linear correlation is found between 3‐methylphthalic anhydride yield and the product of (strong acid/total acidity) and mesopore volume of H‐Y, highlighting the need for balanced catalyst acidity and porosity. The efficient coupling of the dehydration and dehydrogenation steps by varying the zeolite‐to‐Pd/C ratio allowed the competitive decarboxylation reaction to be effectively suppressed, which led to an improved 3‐methylphthalic anhydride/total aromatics selectivity ratio of 80 % (89 % total aromatics yield). The incorporation of Pd nanoparticles in close proximity to the acid sites in bifunctional Pd/H‐Y catalysts also afforded a flexible means to control aromatic products selectivity, as further demonstrated in the aromatization of hydrogenated DA adducts from other diene/dienophile combinations. PMID:27557889

Antioxidant and Anti-Osteoporotic Activities of Aromatic Compounds and Sterols from Hericium erinaceum.

PubMed

Li, Wei; Lee, Sang Hyun; Jang, Hae Dong; Ma, Jin Yeul; Kim, Young Ho

2017-01-11

Hericium erinaceum , commonly called lion's mane mushroom, is a traditional edible mushroom widely used in culinary applications and herbal medicines in East Asian countries. In this study, a new sterol, cerevisterol 6-cinnamate ( 6 ), was isolated from the fruiting bodies of H. erinaceum together with five aromatic compounds 1 - 5 and five sterols 7 - 11 . The chemical structures of these compounds were elucidated using chemical and physical methods and comparison of HRESIMS, ¹D-NMR (¹H, 13 C, and DEPT) and 2D-NMR (COSY, HMQC, HMBC, and NOESY) spectra with previously reported data. The antioxidant and anti-osteoporotic activities of extracts and the isolated compounds 1 - 11 were investigated. All compounds exhibited peroxyl radical-scavenging capacity but only compounds 1 , 3 , and 4 showed potent reducing capacity. Moreover, compounds 1 , 2 , 4 , and 5 showed moderate effects on cellular antioxidant activity and inhibited the receptor activator of nuclear factor κB ligand (RANKL)-induced osteoclastic differentiation. These results suggested that H. erinaceum could be utilized in the development of natural antioxidant and anti-osteoporotic nutraceuticals and functional foods.

Infrared Spectroscopy of Matrix-Isolated Polycyclic Aromatic Compounds and their Ions. 6; Polycyclic Aromatic Nitrogen Heterocycles

NASA Technical Reports Server (NTRS)

Mattioda, A. L.; Hudgins, Douglas M.; Bauschlicher, C. W., Jr.; Rosi, M.; Allamandola, L. J.; DeVincenzi, D. (Technical Monitor)

2002-01-01

The matrix-isolation technique has been employed to measure the mid-infrared spectra of several polycyclic aromatic nitrogen heterocycles in both neutral and cationic forms. The species studied include: 7,8 benzoquinoline (C13H9N); 2-azapyrene (C15H9N); 1- and 2-azabenz(a)anthracene (C17H11N); and 1-, 2-, and 4-azachrysene (also C17H11N). The experimentally measured band frequencies and intensities for each molecule are tabulated and compared with their theoretically calculated values computed using density functional theory at the B3LYP/4-31G level. The overall agreement between experiment and theory is quite good, in keeping with previous investigations involving the parent aromatic hydrocarbons. Several interesting spectroscopic trends are found to accompany nitrogen substitution into the aromatic framework of these compounds. First, for the neutral species, the nitrogen atom produces a significant increase in the total integrated infrared intensity across the 1600 - 1100/cm region and plays an essential role in the molecular vibration that underlies an uncharacteristically intense, discrete feature that is observed near 1400/cm in the spectra of 7,8 benzoquinoline, 1-azabenz(a)anthracene, and 4-azachrysene. The origin of this enhanced infrared activity and the nature of the new 1400/cm vibrational mode are explored. Finally, in contrast to the parent hydrocarbon species, these aromatic nitrogen heterocycles possess a significant permanent dipole moment. Consequently, these dipole moments and the rotational constants are reported for these species in their neutral and ionized forms.

Alkyne Benzannulation Reactions for the Synthesis of Novel Aromatic Architectures.

PubMed

Hein, Samuel J; Lehnherr, Dan; Arslan, Hasan; J Uribe-Romo, Fernando; Dichtel, William R

2017-11-21

Aromatic compounds and polymers are integrated into organic field effect transistors, light-emitting diodes, photovoltaic devices, and redox-flow batteries. These compounds and materials feature increasingly complex designs, and substituents influence energy levels, bandgaps, solution conformation, and crystal packing, all of which impact performance. However, many polycyclic aromatic hydrocarbons of interest are difficult to prepare because their substitution patterns lie outside the scope of current synthetic methods, as strategies for functionalizing benzene are often unselective when applied to naphthalene or larger systems. For example, cross-coupling and nucleophilic aromatic substitution reactions rely on prefunctionalized arenes, and even directed metalation methods most often modify positions near Lewis basic sites. Similarly, electrophilic aromatic substitutions access single regioisomers under substrate control. Cycloadditions provide a convergent route to densely functionalized aromatic compounds that compliment the above methods. After surveying cycloaddition reactions that might be used to modify the conjugated backbone of poly(phenylene ethynylene)s, we discovered that the Asao-Yamamoto benzannulation reaction is notably efficient. Although this reaction had been reported a decade earlier, its scope and usefulness for synthesizing complex aromatic systems had been under-recognized. This benzannulation reaction combines substituted 2-(phenylethynyl)benzaldehydes and substituted alkynes to form 2,3-substituted naphthalenes. The reaction tolerates a variety of sterically congested alkynes, making it well-suited for accessing poly- and oligo(ortho-arylene)s and contorted hexabenzocoronenes. In many cases in which asymmetric benzaldehyde and alkyne cycloaddition partners are used, the reaction is regiospecific based on the electronic character of the alkyne substrate. Recognizing these desirable features, we broadened the substrate scope to include silyl

Polybenzoxazole via aromatic nucleophilic displacement

NASA Technical Reports Server (NTRS)

Hergenrother, Paul M. (Inventor); Connell, John W. (Inventor); Smith, Joseph G., Jr. (Inventor)

1993-01-01

Polybenzoxazoles (PBO) are heterocyclic macromolecules which were first synthesized in a two-step process by the initial formation of aromatic diacid chlorides with bis(o-aminophenol)s through solution condensation of aromatic diacid chlorides with bis(o-aminophenol)s followed by thermal cyclodehydration. Since then several methods were utilized in their synthesis. The most common synthetic method for PBO involves a polycondensation of bis(o-aminophenol)s with aromatic diacid diphenyl esters. Another preparative route involves the solution polycondensation of the hydrochloride salts of bis(o-amino phenol)s with aromatic diacids in polyphosphoric acid. Another synthetic method involves the initial formation of poly(o-hydroxy amide)s from silylated bis(o-aminophenol)s with aromatic diacid chlorides followed by thermal cyclodehydration to PBO. A recent preparative route involves the reaction of aromatic bisphenols with bis(fluorophenyl) benzoxazoles by the displacement reaction to form PBO. The novelty of the present invention is that high molecular weight PBO of new chemical structures are prepared that exhibit a favorable combination of physical and mechanical properties.

Polycyclic aromatic hydrocarbons in sediments and mussels of Corral Bay, south central Chile.

PubMed

Palma-Fleming, Hernan; P, Adalberto J Asencio; Gutierrez, Elena

2004-03-01

PAHs were measured in sediments and mussels (Mytilus chilensis) from Carboneros and Puerto Claro, located in Corral Bay, Valdivia. According to the ratio of phenanthrene/anthracene and fluoranthene/pyrene concentrations, these sites are medium polluted with PAHs originating mainly from pyrolytic sources. Fluoranthene was the major component measured in mussels (3.1-390 ng g(-1) dry weight) and sediments (6.9-74.1 ng g(-1) dry weight). In general, mussels were mainly exposed to the dissolved fraction of the lower molecular weight PAHs (tri- and tetra-aromatics) while the higher molecular ring systems (penta- and hexa-aromatics) were more bioavailable to sediments. Mussel PAHs content was relatively constant, with the exception of the 1999 summer season (March), when higher concentration values were found in both sites; however, PAHs residues in sediments showed a temporal variation.

Anaerobic biodegradation of aromatic compounds.

PubMed

Jothimani, P; Kalaichelvan, G; Bhaskaran, A; Selvaseelan, D Augustine; Ramasamy, K

2003-09-01

Many aromatic compounds and their monomers are existing in nature. Besides they are introduced into the environment by human activity. The conversion of these aromatic compounds is mainly an aerobic process because of the involvement of molecular oxygen in ring fission and as an electron acceptor. Recent literatures indicated that ring fission of monomers and obligomers mainly occurs in anaerobic environments through anaerobic respiration with nitrate, sulphate, carbon dioxide or carbonate as electron acceptors. These anaerobic processes will help to work out the better situation for bioremediation of contaminated environments. While there are plenty of efforts to reduce the release of these chemicals to the environment, already contaminated sites need to be remediated not only to restore the sites but to prevent the leachates spreading to nearby environment. Basically microorganisms are better candidates for breakdown of these compounds because of their wider catalytic mechanisms and the ability to act even in the absence of oxygen. These microbes can be grouped based on their energy mechanisms. Normally, the aerobic counterparts employ the enzymes like mono-and-dioxygenases. The end product is basically catechol, which further may be metabolised to CO2 by means of quinones reductases cycles. In the absense of reductases compounds, the reduced catechols tend to become oxidised to form many quinone compounds. The quinone products are more recalcitrant and lead to other aesthetic problems like colour in water, unpleasant odour, etc. On the contrary, in the reducing environment this process is prevented and in a cascade of pathways, the cleaved products are converted to acetyl co-A to be integrated into other central metabolite paths. The central metabolite of anaerobic degradation is invariably co-A thio-esters of benzoic acid or hydroxy benzoic acid. The benzene ring undergoes various substitution and addition reactions to form chloro-, nitro-, methyl- compounds

Studies on the Simultaneous Formation of Aroma-Active and Toxicologically Relevant Vinyl Aromatics from Free Phenolic Acids during Wheat Beer Brewing.

PubMed

Langos, Daniel; Granvogl, Michael

2016-03-23

During the brewing process of wheat beer, the desired aroma-active vinyl aromatics 2-methoxy-4-vinylphenol and 4-vinylphenol as well as the undesired and toxicologically relevant styrene are formed from their respective precursors, free ferulic acid, p-coumaric acid, and cinnamic acid, deriving from the malts. Analysis of eight commercial wheat beers revealed high concentrations of 2-methoxy-4-vinylphenol and 4-vinylphenol always in parallel with high concentrations of styrene or low concentrations of the odorants in parallel with low styrene concentrations, suggesting a similar pathway. To better understand the formation of these vinyl aromatics, each process step of wheat beer brewing and the use of different strains of Saccharomyces cerevisiae were evaluated. During wort boiling, only a moderate decarboxylation of free phenolic acids and formation of desired and undesired vinyl aromatics were monitored due to the thermal treatment. In contrast, this reaction mainly occurred enzymatically catalyzed during fermentation with S. cerevisiae strain W68 with normal Pof(+) activity (phenolic off-flavor) resulting in a wheat beer eliciting the typical aroma requested by consumers due to high concentrations of 2-methoxy-4-vinylphenol (1790 μg/L) and 4-vinylphenol (937 μg/L). Unfortunately, also a high concentration of undesired styrene (28.3 μg/L) was observed. Using a special S. cerevisiae strain without Pof(+) activity resulted in a significant styrene reduction (

Syngas production over La 0.9Ni yAl 11.95-yO 19-δ catalysts during C 14-alkane partial oxidation: Effects of sulfur and polycyclic aromatic hydrocarbons

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gardner, Todd H.

Partial oxidation studies were conducted over a series of Ni-substituted lanthanum hexaaluminate catalysts, La 0.9Ni yAl 11.95-yO 19-δ (y = 1.0, 0.8, 0.4 and 0.2) to evaluate the effect of higher alkane, sulfur and polycyclic aromatic hydrocarbons using tetradecane (n-C 14), dibenzothiophene (DBT) and 1-methylnapthalene (1-MN) as model reaction compounds. XRD showed the Ni-substituted lanthanum hexaaluminate catalysts to have magnetoplumbite structure. Lattice parameters along the a,b-axis are shown to increase systematically with increasing Ni substitution. The unit cell is also shown to increase systematically with Ni substitution providing clear evidence of Ni 2+ substitution for Al 3+ in the lanthanummore » hexaaluminate lattice. Catalytic activity and product yields were evaluated by temperature programmed surface reaction (TPSR) using n-C 14 partial oxidation as a probe reaction. Between 750 and 900°C, H 2 and CO yields are shown to increase with increasing Ni surface sites while aromatic and olefin yields are shown to decrease. Step response experiments were performed to show the effect of 0.1 wt% 1-MN addition on catalytic activity and performance. As expected, at lower Ni substitution, thermal chemistry predominates suggesting fewer available active Ni sites. At the conditions tested, the site blocking effect is shown to be reversible at all levels of Ni substitution. Similar catalytic behaviors are observed with step response experiments to 50 ppm w/w dibenzothiophene (DBT) where site blocking is shown to produce a concomitantly greater effect on catalytic performance and active site occlusion with catalysts that have less active sites. The step response to DBT is also observed to be reversible. Post analysis of the used catalysts shows that coke deposition is greater on the catalysts with lower Ni substitution.« less

Syngas production over La 0.9Ni yAl 11.95-yO 19-δ catalysts during C 14-alkane partial oxidation: Effects of sulfur and polycyclic aromatic hydrocarbons

DOE PAGES

Gardner, Todd H.

2018-02-07

Partial oxidation studies were conducted over a series of Ni-substituted lanthanum hexaaluminate catalysts, La 0.9Ni yAl 11.95-yO 19-δ (y = 1.0, 0.8, 0.4 and 0.2) to evaluate the effect of higher alkane, sulfur and polycyclic aromatic hydrocarbons using tetradecane (n-C 14), dibenzothiophene (DBT) and 1-methylnapthalene (1-MN) as model reaction compounds. XRD showed the Ni-substituted lanthanum hexaaluminate catalysts to have magnetoplumbite structure. Lattice parameters along the a,b-axis are shown to increase systematically with increasing Ni substitution. The unit cell is also shown to increase systematically with Ni substitution providing clear evidence of Ni 2+ substitution for Al 3+ in the lanthanummore » hexaaluminate lattice. Catalytic activity and product yields were evaluated by temperature programmed surface reaction (TPSR) using n-C 14 partial oxidation as a probe reaction. Between 750 and 900°C, H 2 and CO yields are shown to increase with increasing Ni surface sites while aromatic and olefin yields are shown to decrease. Step response experiments were performed to show the effect of 0.1 wt% 1-MN addition on catalytic activity and performance. As expected, at lower Ni substitution, thermal chemistry predominates suggesting fewer available active Ni sites. At the conditions tested, the site blocking effect is shown to be reversible at all levels of Ni substitution. Similar catalytic behaviors are observed with step response experiments to 50 ppm w/w dibenzothiophene (DBT) where site blocking is shown to produce a concomitantly greater effect on catalytic performance and active site occlusion with catalysts that have less active sites. The step response to DBT is also observed to be reversible. Post analysis of the used catalysts shows that coke deposition is greater on the catalysts with lower Ni substitution.« less

Graphene stabilized ultra-small CuNi nanocomposite with high activity and recyclability toward catalysing the reduction of aromatic nitro-compounds

NASA Astrophysics Data System (ADS)

Fang, Hao; Wen, Ming; Chen, Hanxing; Wu, Qingsheng; Li, Weiying

2015-12-01

Nowadays, it is of great significance and a challenge to design a noble-metal-free catalyst with high activity and a long lifetime for the reduction of aromatic nitro-compounds. Here, a 2D structured nanocomposite catalyst with graphene supported CuNi alloy nanoparticles (NPs) is prepared, and is promising for meeting the requirements of green chemistry. In this graphene/CuNi nanocomposite, the ultra-small CuNi nanoparticles (~2 nm) are evenly anchored on graphene sheets, which is not only a breakthrough in the structures, but also brings about an outstanding performance in activity and stability. Combined with a precise optimization of the alloy ratios, the reaction rate constant of graphene/Cu61Ni39 reached a high level of 0.13685 s-1, with a desirable selectivity as high as 99% for various aromatic nitro-compounds. What's more, the catalyst exhibited a unprecedented long lifetime because it could be recycled over 25 times without obvious performance decay or even a morphology change. This work showed the promise and great potential of noble-metal-free catalysts in green chemistry.Nowadays, it is of great significance and a challenge to design a noble-metal-free catalyst with high activity and a long lifetime for the reduction of aromatic nitro-compounds. Here, a 2D structured nanocomposite catalyst with graphene supported CuNi alloy nanoparticles (NPs) is prepared, and is promising for meeting the requirements of green chemistry. In this graphene/CuNi nanocomposite, the ultra-small CuNi nanoparticles (~2 nm) are evenly anchored on graphene sheets, which is not only a breakthrough in the structures, but also brings about an outstanding performance in activity and stability. Combined with a precise optimization of the alloy ratios, the reaction rate constant of graphene/Cu61Ni39 reached a high level of 0.13685 s-1, with a desirable selectivity as high as 99% for various aromatic nitro-compounds. What's more, the catalyst exhibited a unprecedented long lifetime

Aromatic hydrocarbons from the Middle Jurassic fossil wood of the Polish Jura

NASA Astrophysics Data System (ADS)

Smolarek, Justyna; Marynowski, Leszek

2013-09-01

Aromatic hydrocarbons are present in the fossil wood samples in relatively small amounts. In almost all of the tested samples the dominating aromatic hydrocarbon is perylene and its methyl and dimethyl derivatives. The most important biomarkers present in the aromatic fraction are dehydroabietane, siomonellite and retene, compounds characteristic for conifers. The distribution of discussed compounds is highly variable due to such early diagenetic processes affecting the wood as oxidation and the activity of microorganisms. MPI1 parameter values (methylphenanthrene index) for the majority of the samples are in the range of 0.1 to 0.5, which results in the highly variable values of Rc (converted value of vitrinite reflectance) ranging from 0.45 to 0.70%. Such values suggest that MPI1 parameter is not useful as maturity parameter in case of Middle Jurassic ore-bearing clays, even if measured strictly on terrestrial organic matter (OM). As a result of weathering processes (oxidation) the distribution of aromatic hydrocarbons changes. In the oxidized samples the amount of aromatic hydrocarbons, both polycyclic as well as aromatic biomarkers decreases.

Increase in D-tagatose production rate by site-directed mutagenesis of L-arabinose isomerase from Geobacillus thermodenitrificans.

PubMed

Oh, Hyo-Jung; Kim, Hye-Jung; Oh, Deok-Kun

2006-02-01

Among single-site mutations of L-arabinose isomerase derived from Geobacillus thermodenitrificans, two mutants were produced having the lowest and highest activities of D-tagatose production. Site-directed mutagenesis at these sites showed that the aromatic ring at amino acid 164 and the size of amino acid 475 were important for D-tagatose production. Among double-site mutations, one mutant converted D-galactose into D-tagatose with a yield of 58% whereas the wild type gave 46% D-tagatose conversion after 300 min at 65 degrees C.

Nucleophilic fluorination of aromatic compounds

DOEpatents

Satyamurthy, Nagichettiar; Barrio, Jorge R

2014-03-18

Iodylbenzene derivatives substituted with electron donating as well as electron withdrawing groups on the aromatic ring are used as precursors in aromatic nucleophilic substitution reactions. The iodyl group (IO.sub.2) is regiospecifically substituted by nucleophilic fluoride to provide the corresponding fluoroaryl derivatives. No-carrier-added [F-18]fluoride ion derived from anhydrous [F-18](F/Kryptofix, [F-18]CsF or a quaternary ammonium fluoride (e.g., Me.sub.4NF, Et.sub.4NF, n-Bu.sub.4NF, (PhCH.sub.2).sub.4NF) exclusively substitutes the iodyl moiety in these derivatives and provides high specific activity F-18 labeled fluoroaryl analogs. Iodyl derivatives of a benzothiazole analog and 6-iodyl-L-dopa derivatives have been synthesized as precursors and have been used in the preparation of no-carrier-added [F-18]fluorobenzothiazole as well as 6-[F-18]fluoro-L-dopa.

Size-dependent distribution and inhalation cancer risk of particle-bound polycyclic aromatic hydrocarbons at a typical e-waste recycling and an urban site.

PubMed

Luo, Pei; Bao, Lian-Jun; Li, Shao-Meng; Zeng, Eddy Y

2015-05-01

Atmospheric particle size distribution of polycyclic aromatic hydrocarbons (PAHs) in a typical e-waste recycling zone and an urban site (Guangzhou) in southern China featured a unimodal peak in 0.56-1.8 μm for 4-6 ring PAHs but no obvious peak for 2-3 ring PAHs at both sites. The atmospheric deposition fluxes of PAHs were estimated at 5.4 ± 2.3 μg m(-2) d(-1) in the e-waste recycling zone and 3.1 ± 0.6 μg m(-2) d(-1) in Guangzhou. In addition, dry and wet deposition fluxes of PAHs were dominated by coarse (Dp > 1.8 μm) and fine particles (Dp < 1.8 μm), respectively. Fine particles predominated the deposition of PAHs in the lung. The results estimated by incremental inhalation cancer risk suggested that particle-bound PAHs posed serious threat to human health within the e-waste recycling zone and Guangzhou. Copyright © 2015 Elsevier Ltd. All rights reserved.

Dissecting the active site of a photoreceptor protein

NASA Astrophysics Data System (ADS)

Hoff, Wouter; Hara, Miwa; Ren, Jie; Moghadam, Farzaneh; Xie, Aihua; Kumauchi, Masato

While enzymes are quite large molecules, functionally important chemical events are often limited to a small region of the protein: the active site. The physical and chemical properties of residues at such active sites are often strongly altered compared to the same groups dissolved in water. Understanding such effects is important for unraveling the mechanisms underlying protein function and for protein engineering, but has proven challenging. Here we report on our ongoing efforts on using photoactive yellow protein (PYP), a bacterial photoreceptor, as a model system for such effects. We will report on the following questions: How many residues affect active site properties? Are these residues in direct physical contact with the active site? Can functionally important residues be recognized in the crystal structure of a protein? What structural resolution is needed to understand active sites? What spectroscopic techniques are most informative? Which weak interactions dominate active site properties?

Three-dimensional aromatic networks.

PubMed

Toyota, Shinji; Iwanaga, Tetsuo

2014-01-01

Three-dimensional (3D) networks consisting of aromatic units and linkers are reviewed from various aspects. To understand principles for the construction of such compounds, we generalize the roles of building units, the synthetic approaches, and the classification of networks. As fundamental compounds, cyclophanes with large aromatic units and aromatic macrocycles with linear acetylene linkers are highlighted in terms of transannular interactions between aromatic units, conformational preference, and resolution of chiral derivatives. Polycyclic cage compounds are constructed from building units by linkages via covalent bonds, metal-coordination bonds, or hydrogen bonds. Large cage networks often include a wide range of guest species in their cavity to afford novel inclusion compounds. Topological isomers consisting of two or more macrocycles are formed by cyclization of preorganized species. Some complicated topological networks are constructed by self-assembly of simple building units.

Palladium-catalysed electrophilic aromatic C-H fluorination

NASA Astrophysics Data System (ADS)

Yamamoto, Kumiko; Li, Jiakun; Garber, Jeffrey A. O.; Rolfes, Julian D.; Boursalian, Gregory B.; Borghs, Jannik C.; Genicot, Christophe; Jacq, Jérôme; van Gastel, Maurice; Neese, Frank; Ritter, Tobias

2018-02-01

Aryl fluorides are widely used in the pharmaceutical and agrochemical industries, and recent advances have enabled their synthesis through the conversion of various functional groups. However, there is a lack of general methods for direct aromatic carbon-hydrogen (C-H) fluorination. Conventional methods require the use of either strong fluorinating reagents, which are often unselective and difficult to handle, such as elemental fluorine, or less reactive reagents that attack only the most activated arenes, which reduces the substrate scope. A method for the direct fluorination of aromatic C-H bonds could facilitate access to fluorinated derivatives of functional molecules that would otherwise be difficult to produce. For example, drug candidates with improved properties, such as increased metabolic stability or better blood-brain-barrier penetration, may become available. Here we describe an approach to catalysis and the resulting development of an undirected, palladium-catalysed method for aromatic C-H fluorination using mild electrophilic fluorinating reagents. The reaction involves a mode of catalysis that is unusual in aromatic C-H functionalization because no organometallic intermediate is formed; instead, a reactive transition-metal-fluoride electrophile is generated catalytically for the fluorination of arenes that do not otherwise react with mild fluorinating reagents. The scope and functional-group tolerance of this reaction could provide access to functional fluorinated molecules in pharmaceutical and agrochemical development that would otherwise not be readily accessible.

Adsorption of aromatic hydrocarbons and ozone at environmental aqueous surfaces.

PubMed

Vácha, Robert; Cwiklik, Lukasz; Rezác, Jan; Hobza, Pavel; Jungwirth, Pavel; Valsaraj, Kalliat; Bahr, Stephan; Kempter, Volker

2008-06-05

Adsorption of environmentally important aromatic molecules on a water surface is studied by means of classical and ab initio molecular dynamics simulations and by reflection-absorption infrared spectroscopy. Both techniques show strong activity and orientational preference of these molecules at the surface. Benzene and naphthalene, which bind weakly to water surface with a significant contribution of dispersion interactions, prefer to lie flat on water but retain a large degree of orientational flexibility. Pyridine is more rigid at the surface. It is tilted with the nitrogen end having strong hydrogen bonding interactions with water molecules. The degree of adsorption and orientation of aromatic molecules on aqueous droplets has atmospheric implications for heterogeneous ozonolysis, for which the Langmuir-Hinshelwood kinetics mechanism is discussed. At higher coverages of aromatic molecules the incoming ozone almost does not come into contact with the underlying aqueous phase. This may rationalize the experimental insensitivity of the ozonolysis on the chemical nature of the substrate on which the aromatic molecules adsorb.

Active site dynamics of ribonuclease.

PubMed Central

Brünger, A T; Brooks, C L; Karplus, M

1985-01-01

The stochastic boundary molecular dynamics method is used to study the structure, dynamics, and energetics of the solvated active site of bovine pancreatic ribonuclease A. Simulations of the native enzyme and of the enzyme complexed with the dinucleotide substrate CpA and the transition-state analog uridine vanadate are compared. Structural features and dynamical couplings for ribonuclease residues found in the simulation are consistent with experimental data. Water molecules, most of which are not observed in crystallographic studies, are shown to play an important role in the active site. Hydrogen bonding of residues with water molecules in the free enzyme is found to mimic the substrate-enzyme interactions of residues involved in binding. Networks of water stabilize the cluster of positively charged active site residues. Correlated fluctuations between the uridine vanadate complex and the distant lysine residues are mediated through water and may indicate a possible role for these residues in stabilizing the transition state. Images PMID:3866234

Non-ovarian aromatization is required to activate female sexual motivation in testosterone-treated ovariectomized quail

PubMed Central

de Bournonville, Catherine; Balthazart, Jacques; Ball, Gregory F.; Cornil, Charlotte A.

2016-01-01

Although aromatase is expressed in both male and female brains, its functional significance in females remains poorly understood. In female quail, sexual receptivity is activated by estrogens. However it is not known whether sexual motivation is similarly estrogen-dependent and whether estrogens locally produced in the brain contribute to these behavioral responses. Four main experiments were designed to address these questions. In experiment 1 chronic treatment of females with the anti-estrogen tamoxifen decreased their receptivity, confirming that this response is under the control of estrogens. In experiment 2 chronic treatment with tamoxifen significantly decreased sexual motivation as treated females no longer approached a sexual partner. In experiment 3 (a) ovariectomy (OVX) induced a significant decrease of time spent near the male and a significantly decreased receptivity compared to gonadally intact females, (b) treatment with testosterone (OVX+T) partially restored these responses and (c) this effect of T was prevented when estradiol synthesis was inhibited by the potent aromatase inhibitor Vorozole (OVX+T+VOR). Serum estradiol concentration was significantly higher in OVX+T than in OVX or OVX+T+VOR females. Together these data demonstrate that treatment of OVX females with T increases sexual motivation and that these effects are mediated at least in part by non-gonadal aromatization of the androgen. Finally, assays of aromatase activity on brain and peripheral tissues (Experiment 4) strongly suggest that brain aromatization contributes to behavioral effects observed here following T treatment but alternative sources of estrogens (e.g. liver) should also be considered. PMID:27189762

Low dielectric response in enzyme active site

PubMed Central

Mertz, Edward L.; Krishtalik, Lev I.

2000-01-01

The kinetics of charge transfer depend crucially on the dielectric reorganization of the medium. In enzymatic reactions that involve charge transfer, atomic dielectric response of the active site and of its surroundings determines the efficiency of the protein as a catalyst. We report direct spectroscopic measurements of the reorganization energy associated with the dielectric response in the active site of α-chymotrypsin. A chromophoric inhibitor of the enzyme is used as a spectroscopic probe. We find that water strongly affects the dielectric reorganization in the active site of the enzyme in solution. The reorganization energy of the protein matrix in the vicinity of the active site is similar to that of low-polarity solvents. Surprisingly, water exhibits an anomalously high dielectric response that cannot be described in terms of the dielectric continuum theory. As a result, sequestering the active site from the aqueous environment inside low-dielectric enzyme body dramatically reduces the dielectric reorganization. This reduction is particularly important for controlling the rate of enzymatic reactions. PMID:10681440

Presence and potential significance of aromatic-ketone groups in aquatic humic substances

USGS Publications Warehouse

Leenheer, J.A.; Wilson, M.A.; Malcolm, R.L.

1987-01-01

Aquatic humic- and fulvic-acid standards of the International Humic Substances Society were characterized, with emphasis on carbonyl-group nature and content, by carbon-13 nuclear-magnetic-resonance spectroscopy, proton nuclear-magnetic-resonance spectroscopy, and infrared spectroscopy. After comparing spectral results of underivatized humic and fulvic acids with spectral results of chemically modified derivatives, that allow improved observation of the carbonyl group, the data clearly indicated that aromatic ketone groups comprised the majority of the carbonyl-group content. About one ketone group per monocyclic aromatic ring was determined for both humic and fulvic acids. Aromatic-ketone groups were hypothesized to form by photolytic rearrangements and oxidation of phenolic ester and hydrocarbon precursors; these groups have potential significance regarding haloform formation in water, reactivity resulting from active hydrogen of the methyl and methylene adjacent to the ketone groups, and formation of hemiketal and lactol structures. Aromatic-ketone groups also may be the point of attachment between aliphatic and aromatic moieties of aquatic humic-substance structure. ?? 1987.

Methanopyrus kandleri topoisomerase V contains three distinct AP lyase active sites in addition to the topoisomerase active site

PubMed Central

Rajan, Rakhi; Osterman, Amy; Mondragón, Alfonso

2016-01-01

Topoisomerase V (Topo-V) is the only topoisomerase with both topoisomerase and DNA repair activities. The topoisomerase activity is conferred by a small alpha-helical domain, whereas the AP lyase activity is found in a region formed by 12 tandem helix-hairpin-helix ((HhH)2) domains. Although it was known that Topo-V has multiple repair sites, only one had been mapped. Here, we show that Topo-V has three AP lyase sites. The atomic structure and Small Angle X-ray Scattering studies of a 97 kDa fragment spanning the topoisomerase and 10 (HhH)2 domains reveal that the (HhH)2 domains extend away from the topoisomerase domain. A combination of biochemical and structural observations allow the mapping of the second repair site to the junction of the 9th and 10th (HhH)2 domains. The second site is structurally similar to the first one and to the sites found in other AP lyases. The 3rd AP lyase site is located in the 12th (HhH)2 domain. The results show that Topo-V is an unusual protein: it is the only known protein with more than one (HhH)2 domain, the only known topoisomerase with dual activities and is also unique by having three AP lyase repair sites in the same polypeptide. PMID:26908655

Risk Assessment Related to Atmospheric Polycyclic Aromatic Hydrocarbons in Gas and Particle Phases near Industrial Sites

PubMed Central

Ramírez, Noelia; Cuadras, Anna; Marcé, Rosa Maria

2011-01-01

Background: Inhalation is one of the main means of human exposure to polycyclic aromatic hydrocarbons (PAHs) because of their ubiquitous presence in the atmosphere. However, most studies have considered only PAHs found in the particle phase and have omitted the contribution of the gas-phase PAHs to the risk. Objective: We estimated the lifetime lung cancer risk from PAH exposure by inhalation in people living next to the largest chemical site in Southern Europe and the Mediterranean area. Methods: We determined 18 PAHs in the atmospheric gas and particle phase. We monitored the PAHs for 1 year in three locations near the chemical site in different seasons. We used toxic equivalence factors to calculate benzo[a]pyrene (BaP) equivalents (BaP-eq) for individual PAHs and applied the World Health Organization unit risk (UR) for BaP (UR = 8.7 × 10–5) to estimate lifetime cancer risks due to PAH exposures. Results: We observed some spatial and seasonal variability in PAH concentrations. The contribution of gas-phase PAHs to the total BaP-eq value was between 34% and 86%. The total estimated average lifetime lung cancer risk due to PAH exposure in the study area was 1.2 × 10–4. Conclusions: The estimated risk was higher than values recommended by the World Health Organization and U.S. Environmental Protection Agency but lower than the threshold value of 10–3 that is considered an indication of definite risk according to similar risk studies. The results also showed that risk may be underestimated if the contributions of gas-phase PAHs are not considered. PMID:21478082

Graphene stabilized ultra-small CuNi nanocomposite with high activity and recyclability toward catalysing the reduction of aromatic nitro-compounds.

PubMed

Fang, Hao; Wen, Ming; Chen, Hanxing; Wu, Qingsheng; Li, Weiying

2016-01-07

Nowadays, it is of great significance and a challenge to design a noble-metal-free catalyst with high activity and a long lifetime for the reduction of aromatic nitro-compounds. Here, a 2D structured nanocomposite catalyst with graphene supported CuNi alloy nanoparticles (NPs) is prepared, and is promising for meeting the requirements of green chemistry. In this graphene/CuNi nanocomposite, the ultra-small CuNi nanoparticles (∼2 nm) are evenly anchored on graphene sheets, which is not only a breakthrough in the structures, but also brings about an outstanding performance in activity and stability. Combined with a precise optimization of the alloy ratios, the reaction rate constant of graphene/Cu61Ni39 reached a high level of 0.13685 s(-1), with a desirable selectivity as high as 99% for various aromatic nitro-compounds. What's more, the catalyst exhibited a unprecedented long lifetime because it could be recycled over 25 times without obvious performance decay or even a morphology change. This work showed the promise and great potential of noble-metal-free catalysts in green chemistry.

Experimental Determination of Activation Energy of Nucleophilic Aromatic Substitution on Porphyrins

ERIC Educational Resources Information Center

Rizvi, Waqar; Khwaja, Emaad; Siddiqui, Saim; Bhupathiraju, N. V. S. Dinesh K.; Drain, Charles Michael

2018-01-01

A physical organic chemistry experiment is described for second-year college students. Students performed nucleophilic aromatic substitution (NAS) reactions on 5,10,15,20-tetrakis(2,3,4,5,6-pentafluorophenyl)porphyrin (TPPF[subscript 20]) using three different nucleophiles. Substitution occurs preferentially at the 4-position ("para")…

A two-helix motif positions the active site of lysophosphatidic acid acyltransferase for catalysis within the membrane bilayer

PubMed Central

Robertson, Rosanna M.; Yao, Jiangwei; Gajewski, Stefan; Kumar, Gyanendra; Martin, Erik W.; Rock, Charles O.; White, Stephen W.

2017-01-01

Phosphatidic acid is the central intermediate in membrane phospholipid synthesis and is generated by two acyltransferases in a pathway conserved in all life forms. The second step in this pathway is catalyzed by 1-acyl-sn-glycero-3-phosphate acyltransferase, called PlsC in bacteria. The crystal structure of PlsC from Thermotoga maritima reveals an unusual hydrophobic/aromatic N-terminal two-helix motif linked to an acyltransferase αβ domain that contains the catalytic HX4D motif. PlsC dictates the acyl chain composition of the 2-position of phospholipids, and the acyl chain selectivity ‘ruler’ is an appropriately placed and closed hydrophobic tunnel. This was confirmed by site-directed mutagenesis and membrane composition analysis of Escherichia coli cells expressing the mutated proteins. MD simulations reveal that the two-helix motif represents a novel substructure that firmly anchors the protein to one leaflet of the membrane. This binding mode allows the PlsC active site to acylate lysophospholipids within the membrane bilayer using soluble acyl donors. PMID:28714993

Birds and polycyclic aromatic hydrocarbons

USGS Publications Warehouse

Albers, P.H.

2006-01-01

Polycyclic aromatic hydrocarbons (PAH) are present throughout the global environment and are produced naturally and by activities of humans. Effects of PAH on birds have been determined by studies employing egg injection, egg immersion, egg shell application, single and multiple oral doses, subcutaneous injection, and chemical analysis of field-collected eggs and tissue. The four-to six-ring aromatic compounds are the most toxic to embryos, young birds, and adult birds. For embryos, effects include death, developmental abnormalities, and a variety of cellular and biochemical responses. For adult and young birds, effects include reduced egg production and hatching, increased clutch or brood abandonment, reduced growth, increased organweights, and a variety of biochemical responses. Trophic level accumulation is unlikely. Environmental exposure to PAH in areas of high human population or habitats affected by recent petroleum spills might be sufficient to adversely affect reproduction. Evidence of long-term effects of elevated concentrations of environmental PAH on bird populations is very limited and the mechanisms of effect are unclear.

The molecular biology of environmental aromatic hydrocarbons

DOE Office of Scientific and Technical Information (OSTI.GOV)

Weiss, S.B.

The induction of mutations in living cells by polycyclic aromatic hydrocarbons (PAH) has been recognized for many years. Although the mechanism for this occurrence has been examined by numerous investigators, the precise nature and type of mutations induced is still unclear. Earlier investigations of DNA damage and repair were primarily examined by the random alkylation of bacterial and mammalian DNAs, in vivo, using a variety of different PAH agents. This procedure is still used today. Though informative, such studies have not offered any explanation of the mechanism by which PAH agents induce carcinogenesis. We have attempted to examine the repairmore » of PAH-damaged DNA using small DNA oligomer constructs as targets for site-specific alkylation. DNA constructs containing a single BPDE alkylated site in each duplex strand were ligated into M13 RF DNA and used to transfect E. coli. Progeny M13 DNA was isolated from E. coli colonies grown on agar plates containing IPTG and Xgal. DNA sequence analysis of the isolated progeny M13 DNA, at the site of construct insertion, was found to contain large deletions and illegitimate recombinants. These sequence rearrangements occurred in either recA{sup +} or recA{sup -} host cells suggesting that SOS processing was not involved in the deletions and the recombinants observed. The mechanism by which BPDE induces illegitimate recombinants has not been resolved, however, it is possible that the closely spaced adducts activate the recombinant machinery in our DNA-damaged cells. 1 ref., 6 figs., 1 tab.« less

Strong CH/O interactions between polycyclic aromatic hydrocarbons and water: Influence of aromatic system size.

PubMed

Veljković, Dušan Ž

2018-03-01

Energies of CH/O interactions between water molecule and polycyclic aromatic hydrocarbons with a different number of aromatic rings were calculated using ab initio calculations at MP2/cc-PVTZ level. Results show that an additional aromatic ring in structure of polycyclic aromatic hydrocarbons significantly strengthens CH/O interactions. Calculated interaction energies in optimized structures of the most stable tetracene/water complex is -2.27 kcal/mol, anthracene/water is -2.13 kcal/mol and naphthalene/water is -1.97 kcal/mol. These interactions are stronger than CH/O contacts in benzene/water complex (-1.44 kcal/mol) while CH/O contacts in tetracene/water complex are even stronger than CH/O contacts in pyridine/water complexes (-2.21 kcal/mol). Electrostatic potential maps for different polycyclic aromatic hydrocarbons were calculated and used to explain trends in the energies of interactions. Copyright © 2017 Elsevier Inc. All rights reserved.

Application of molecular docking and ONIOM methods for the description of interactions between anti-quorum sensing active (AHL) analogues and the Pseudomonas aeruginosa LasR binding site.

PubMed

Ahumedo, Maicol; Drosos, Juan Carlos; Vivas-Reyes, Ricardo

2014-05-01

Molecular docking methods were applied to simulate the coupling of a set of nineteen acyl homoserine lactone analogs into the binding site of the transcriptional receptor LasR. The best pose of each ligand was explored and a qualitative analysis of the possible interactions present in the complex was performed. From the results of the protein-ligand complex analysis, it was found that residues Tyr-64 and Tyr-47 are involved in important interactions, which mainly determine the antagonistic activity of the AHL analogues considered for this study. The effect of different substituents on the aromatic ring, the common structure to all ligands, was also evaluated focusing on how the interaction with the two previously mentioned tyrosine residues was affected. Electrostatic potential map calculations based on the electron density and the van der Waals radii were performed on all ligands to graphically aid in the explanation of the variation of charge density on their structures when the substituent on the aromatic ring is changed through the elements of the halogen group series. A quantitative approach was also considered and for that purpose the ONIOM method was performed to estimate the energy change in the different ligand-receptor complex regions. Those energy values were tested for their relationship with the corresponding IC50 in order to establish if there is any correlation between energy changes in the selected regions and the biological activity. The results obtained using the two approaches may contribute to the field of quorum sensing active molecules; the docking analysis revealed the role of some binding site residues involved in the formation of a halogen bridge with ligands. These interactions have been demonstrated to be responsible for the interruption of the signal propagation needed for the quorum sensing circuit. Using the other approach, the structure-activity relationship (SAR) analysis, it was possible to establish which structural characteristics

Remarkably selective iridium catalysts for the elaboration of aromatic C-H bonds.

PubMed

Cho, Jian-Yang; Tse, Man Kin; Holmes, Daniel; Maleczka, Robert E; Smith, Milton R

2002-01-11

Arylboron compounds have intriguing properties and are important building blocks for chemical synthesis. A family of Ir catalysts now enables the direct synthesis of arylboron compounds from aromatic hydrocarbons and boranes under "solventless" conditions. The Ir catalysts are highly selective for C-H activation and do not interfere with subsequent in situ transformations, including Pd-mediated cross-couplings with aryl halides. By virtue of their favorable activities and exceptional selectivities, these Ir catalysts impart the synthetic versatility of arylboron reagents to C-H bonds in aromatic and heteroaromatic hydrocarbons.

Fluorescent aromatic sensors and their methods of use

NASA Technical Reports Server (NTRS)

Meador, Michael A. (Inventor); Tyson, Daniel S. (Inventor); Ilan, Ulvi F. (Inventor)

2012-01-01

Aromatic molecules that can be used as sensors are described. The aromatic sensors include a polycyclic aromatic hydrocarbon core with a five-membered imide rings fused to the core and at least two pendant aryl groups. The aromatic sensor molecules can detect target analytes or molecular strain as a result of changes in their fluorescence, in many cases with on-off behavior. Aromatic molecules that fluoresce at various frequencies can be prepared by altering the structure of the aromatic core or the substituents attached to it. The aromatic molecules can be used as sensors for various applications such as, for example, the detection of dangerous chemicals, biomedical diagnosis, and the detection of damage or strain in composite materials. Methods of preparing aromatic sensor molecules are also described.

Environmental assessment of aromatic hydrocarbons-contaminated sediments of the Mexican Salina Cuz Bay.

PubMed

González-Macías, C; Schifter, I; Lluch-Cota, D B; Méndez-Rodríguez, L; Hernández-Vázquez, S

2007-10-01

Concentrations of total aromatic hydrocarbons and extractable organic matter in the water column and sediment were determined in samples collected in the course of the last 20 years from the Salina Cruz Harbor, México, to assess the degree of organic contamination. In sediments, organic compounds accumulate in shallow areas mostly associated with extractable organic matter and fine fractions. Calculated geocumulation index and enrichment factors suggest that contamination could be derived from anthropogenic activities attributed to harbor and ship scrapping activities, as well as transboundary source. Concentration of total aromatic hydrocarbons (as chrysene equivalents) ranged from 0.01 to 534 microg l(-1) in water, and from 0.10 to 2,160 microg g(-1) in sediments. Total aromatic concentration of 5 microg g(-1) is proposed as background concentration.

Identification of a Long-range Protein Network That Modulates Active Site Dynamics in Extremophilic Alcohol Dehydrogenases*

PubMed Central

Nagel, Zachary D.; Cun, Shujian; Klinman, Judith P.

2013-01-01

A tetrameric thermophilic alcohol dehydrogenase from Bacillus stearothermophilus (ht-ADH) has been mutated at an aromatic side chain in the active site (Trp-87). The ht-W87A mutation results in a loss of the Arrhenius break seen at 30 °C for the wild-type enzyme and an increase in cold lability that is attributed to destabilization of the active tetrameric form. Kinetic isotope effects (KIEs) are nearly temperature-independent over the experimental temperature range, and similar in magnitude to those measured above 30 °C for the wild-type enzyme. This suggests that the rigidification in the wild-type enzyme below 30 °C does not occur for ht-W87A. A mutation at the dimer-dimer interface in a thermolabile psychrophilic homologue of ht-ADH, ps-A25Y, leads to a more thermostable enzyme and a change in the rate-determining step at low temperature. The reciprocal mutation in ht-ADH, ht-Y25A, results in kinetic behavior similar to that of W87A. Collectively, the results indicate that flexibility at the active site is intimately connected to a subunit interaction 20 Å away. The convex Arrhenius curves previously reported for ht-ADH (Kohen, A., Cannio, R., Bartolucci, S., and Klinman, J. P. (1999) Nature 399, 496–499) are proposed to arise, at least in part, from a change in subunit interactions that rigidifies the substrate-binding domain below 30 °C, and impedes the ability of the enzyme to sample the catalytically relevant conformational landscape. These results implicate an evolutionarily conserved, long-range network of dynamical communication that controls C-H activation in the prokaryotic alcohol dehydrogenases. PMID:23525111

Conformationally restrained aromatic analogues of fosmidomycin and FR900098.

PubMed

Kurz, Thomas; Schlüter, Katrin; Pein, Miriam; Behrendt, Christoph; Bergmann, Bärbel; Walter, Rolf D

2007-07-01

The synthesis and in-vitro antimalarial activity of conformationally restrained bis(pivaloyloxymethyl) ester analogues of the natural product fosmidomycin is presented. In contrast to alpha-aryl-substituted analogues, conformationally restrained aromatic analogues exhibit only moderate in-vitro antimalarial activity against the chloroquine-sensitive strain 3D7 of Plasmodium falciparum. The most active derivative displays an IC(50) value of 47 microM.

Concentrations of polycyclic aromatic hydrocarbons: Their potential health risks and sources at three non-urban sites in Japan.

PubMed

Jadoon, Waqar A; Sakugawa, Hiroshi

2016-09-18

This investigation was undertaken to monitor particulate polycyclic aromatic hydrocarbons (PAHs) concentrations in order to determine their emission sources and potential human health risks in remote and rural areas of Japan. Seventeen PAHs in aerosol samples collected in remote (Kamihaya), coastal (Hiki) and inland (Higashi-Hiroshima) areas of Japan during 2013-2014 were analyzed using gas chromatography/mass spectrometry. Total PAH (Σ17PAH) concentrations in aerosol samples were in the range of 0.08-6.51 ng m(-3), 0.09-4.74 ng m(-3), and 0.21-6.53 ng m(-3) at Kamihaya, Hiki, and Higashi-Hiroshima sites, with mean concentrations of 1.63, 1.18, and 2.43 ng m(-3), respectively. Significant seasonal variation in concentrations occurred at Hiki and Higashi-Hiroshima, while no significant variation occurred at Kamihaya. Ambient air temperature greatly affected PAH concentrations in Higashi-Hiroshima, but had only moderate effects in Kamihaya and Hiki. Wind direction also influenced the concentrations of PAHs. Vehicle exhaust, industrial emissions, biomass combustion, and domestic heating and cooking were identified as the main PAH emission sources using principal component analysis. Backward trajectory calculations showed that domestically generated PAHs were significant in Kamihaya and Hiki, while in Higashi-Hiroshima concentrations were mainly influenced by long-range transport. The incremental lifetime lung cancer risk had values of 3.38 × 10(-5) and 1.84 × 10(-5) at Higashi-Hiroshima and Hiki, which are greater than the US EPA acceptable level (10(-6)). Typically, 5-6-ring PAHs contributed 95% to this overall health risk, of which benzo(a)pyrene was the largest contributor, followed by dibenz(a,h)anthracene at both residential sites. Clearly, stricter guidelines for PAHs need to be implemented at these sites to protect the population.

Naringin directly activates inwardly rectifying potassium channels at an overlapping binding site to tertiapin-Q

PubMed Central

Yow, Tin T; Pera, Elena; Absalom, Nathan; Heblinski, Marika; Johnston, Graham AR; Hanrahan, Jane R; Chebib, Mary

2011-01-01

BACKGROUND G protein-coupled inwardly rectifying potassium (KIR3) channels are important proteins that regulate numerous physiological processes including excitatory responses in the CNS and the control of heart rate. Flavonoids have been shown to have significant health benefits and are a diverse source of compounds for identifying agents with novel mechanisms of action. EXPERIMENTAL APPROACH The flavonoid glycoside, naringin, was evaluated on recombinant human KIR3.1–3.4 and KIR3.1–3.2 expressed in Xenopus oocytes using two-electrode voltage clamp methods. In addition, we evaluated the activity of naringin alone and in the presence of the KIR3 channel blocker tertiapin-Q (0.5 nM, 1 nM and 3 nM) at recombinant KIR3.1–3.4 channels. Site-directed mutagenesis was used to identify amino acids within the M1–M2 loop of the KIR3.1F137S mutant channel important for naringin's activity. KEY RESULTS Naringin (100 µM) had minimal effect on uninjected oocytes but activated KIR3.1–3.4 and KIR3.1–3.2 channels. The activation by naringin of KIR3.1–3.4 channels was inhibited by tertiapin-Q in a competitive manner. An alanine-scan performed on the KIR3.1F137S mutant channel, replacing one by one aromatic amino acids within the M1–M2 loop, identified tyrosines 148 and 150 to be significantly contributing to the affinity of naringin as these mutations reduced the activity of naringin by 20- and 40-fold respectively. CONCLUSIONS AND IMPLICATIONS These results show that naringin is a direct activator of KIR3 channels and that tertiapin-Q shares an overlapping binding site on the KIR3.1–3.4. This is the first example of a ligand that activates KIR3 channels by binding to the extracellular M1–M2 linker of the channel. PMID:21391982

Activation of phenylalanine hydroxylase by phenylalanine does not require binding in the active site.

PubMed

Roberts, Kenneth M; Khan, Crystal A; Hinck, Cynthia S; Fitzpatrick, Paul F

2014-12-16

Phenylalanine hydroxylase (PheH), a liver enzyme that catalyzes the hydroxylation of excess phenylalanine in the diet to tyrosine, is activated by phenylalanine. The lack of activity at low levels of phenylalanine has been attributed to the N-terminus of the protein's regulatory domain acting as an inhibitory peptide by blocking substrate access to the active site. The location of the site at which phenylalanine binds to activate the enzyme is unknown, and both the active site in the catalytic domain and a separate site in the N-terminal regulatory domain have been proposed. Binding of catecholamines to the active-site iron was used to probe the accessibility of the active site. Removal of the regulatory domain increases the rate constants for association of several catecholamines with the wild-type enzyme by ∼2-fold. Binding of phenylalanine in the active site is effectively abolished by mutating the active-site residue Arg270 to lysine. The k(cat)/K(phe) value is down 10⁴ for the mutant enzyme, and the K(m) value for phenylalanine for the mutant enzyme is >0.5 M. Incubation of the R270K enzyme with phenylalanine also results in a 2-fold increase in the rate constants for catecholamine binding. The change in the tryptophan fluorescence emission spectrum seen in the wild-type enzyme upon activation by phenylalanine is also seen with the R270K mutant enzyme in the presence of phenylalanine. Both results establish that activation of PheH by phenylalanine does not require binding of the amino acid in the active site. This is consistent with a separate allosteric site, likely in the regulatory domain.

Activation of Phenylalanine Hydroxylase by Phenylalanine Does Not Require Binding in the Active Site

PubMed Central

2015-01-01

Phenylalanine hydroxylase (PheH), a liver enzyme that catalyzes the hydroxylation of excess phenylalanine in the diet to tyrosine, is activated by phenylalanine. The lack of activity at low levels of phenylalanine has been attributed to the N-terminus of the protein’s regulatory domain acting as an inhibitory peptide by blocking substrate access to the active site. The location of the site at which phenylalanine binds to activate the enzyme is unknown, and both the active site in the catalytic domain and a separate site in the N-terminal regulatory domain have been proposed. Binding of catecholamines to the active-site iron was used to probe the accessibility of the active site. Removal of the regulatory domain increases the rate constants for association of several catecholamines with the wild-type enzyme by ∼2-fold. Binding of phenylalanine in the active site is effectively abolished by mutating the active-site residue Arg270 to lysine. The kcat/Kphe value is down 104 for the mutant enzyme, and the Km value for phenylalanine for the mutant enzyme is >0.5 M. Incubation of the R270K enzyme with phenylalanine also results in a 2-fold increase in the rate constants for catecholamine binding. The change in the tryptophan fluorescence emission spectrum seen in the wild-type enzyme upon activation by phenylalanine is also seen with the R270K mutant enzyme in the presence of phenylalanine. Both results establish that activation of PheH by phenylalanine does not require binding of the amino acid in the active site. This is consistent with a separate allosteric site, likely in the regulatory domain. PMID:25453233

Non-competitive inhibition by active site binders.

PubMed

Blat, Yuval

2010-06-01

Classical enzymology has been used for generations to understand the interactions of inhibitors with their enzyme targets. Enzymology tools enabled prediction of the biological impact of inhibitors as well as the development of novel, more potent, ones. Experiments designed to examine the competition between the tested inhibitor and the enzyme substrate(s) are the tool of choice to identify inhibitors that bind in the active site. Competition between an inhibitor and a substrate is considered a strong evidence for binding of the inhibitor in the active site, while the lack of competition suggests binding to an alternative site. Nevertheless, exceptions to this notion do exist. Active site-binding inhibitors can display non-competitive inhibition patterns. This unusual behavior has been observed with enzymes utilizing an exosite for substrate binding, isomechanism enzymes, enzymes with multiple substrates and/or products and two-step binding inhibitors. In many of these cases, the mechanisms underlying the lack of competition between the substrate and the inhibitor are well understood. Tools like alternative substrates, testing the enzyme reaction in the reverse direction and monitoring inhibition time dependence can be applied to enable distinction between 'badly behaving' active site binders and true exosite inhibitors.

Safety Oversight of Decommissioning Activities at DOE Nuclear Sites

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zull, Lawrence M.; Yeniscavich, William

2008-01-15

The Defense Nuclear Facilities Safety Board (Board) is an independent federal agency established by Congress in 1988 to provide nuclear safety oversight of activities at U.S. Department of Energy (DOE) defense nuclear facilities. The activities under the Board's jurisdiction include the design, construction, startup, operation, and decommissioning of defense nuclear facilities at DOE sites. This paper reviews the Board's safety oversight of decommissioning activities at DOE sites, identifies the safety problems observed, and discusses Board initiatives to improve the safety of decommissioning activities at DOE sites. The decommissioning of former defense nuclear facilities has reduced the risk of radioactive materialmore » contamination and exposure to the public and site workers. In general, efforts to perform decommissioning work at DOE defense nuclear sites have been successful, and contractors performing decommissioning work have a good safety record. Decommissioning activities have recently been completed at sites identified for closure, including the Rocky Flats Environmental Technology Site, the Fernald Closure Project, and the Miamisburg Closure Project (the Mound site). The Rocky Flats and Fernald sites, which produced plutonium parts and uranium materials for defense needs (respectively), have been turned into wildlife refuges. The Mound site, which performed R and D activities on nuclear materials, has been converted into an industrial and technology park called the Mound Advanced Technology Center. The DOE Office of Legacy Management is responsible for the long term stewardship of these former EM sites. The Board has reviewed many decommissioning activities, and noted that there are valuable lessons learned that can benefit both DOE and the contractor. As part of its ongoing safety oversight responsibilities, the Board and its staff will continue to review the safety of DOE and contractor decommissioning activities at DOE defense nuclear sites.« less

Aromatic Anchor at an Invariant Hormone-Receptor Interface

PubMed Central

Pandyarajan, Vijay; Smith, Brian J.; Phillips, Nelson B.; Whittaker, Linda; Cox, Gabriella P.; Wickramasinghe, Nalinda; Menting, John G.; Wan, Zhu-li; Whittaker, Jonathan; Ismail-Beigi, Faramarz; Lawrence, Michael C.; Weiss, Michael A.

2014-01-01

Crystallographic studies of insulin bound to fragments of the insulin receptor have recently defined the topography of the primary hormone-receptor interface. Here, we have investigated the role of PheB24, an invariant aromatic anchor at this interface and site of a human mutation causing diabetes mellitus. An extensive set of B24 substitutions has been constructed and tested for effects on receptor binding. Although aromaticity has long been considered a key requirement at this position, MetB24 was found to confer essentially native affinity and bioactivity. Molecular modeling suggests that this linear side chain can serve as an alternative hydrophobic anchor at the hormone-receptor interface. These findings motivated further substitution of PheB24 by cyclohexanylalanine (Cha), which contains a nonplanar aliphatic ring. Contrary to expectations, [ChaB24]insulin likewise exhibited high activity. Furthermore, its resistance to fibrillation and the rapid rate of hexamer disassembly, properties of potential therapeutic advantage, were enhanced. The crystal structure of the ChaB24 analog, determined as an R6 zinc-stabilized hexamer at a resolution of 1.5 Å, closely resembles that of wild-type insulin. The nonplanar aliphatic ring exhibits two chair conformations with partial occupancies, each recapitulating the role of PheB24 at the dimer interface. Together, these studies have defined structural requirements of an anchor residue within the B24-binding pocket of the insulin receptor; similar molecular principles are likely to pertain to insulin-related growth factors. Our results highlight in particular the utility of nonaromatic side chains as probes of the B24 pocket and suggest that the nonstandard Cha side chain may have therapeutic utility. PMID:25305014

Benzoyl radicals from (hetero)aromatic aldehydes. Decatungstate photocatalyzed synthesis of substituted aromatic ketones.

PubMed

Ravelli, Davide; Zema, Michele; Mella, Mariella; Fagnoni, Maurizio; Albini, Angelo

2010-09-21

Benzoyl radicals are generated directly from (hetero)aromatic aldehydes upon tetrabutylammonium decatungstate ((n-Bu(4)N)(4)W(10)O(32)), TBADT) photocatalysis under mild conditions. In the presence of alpha,beta-unsaturated esters, ketones and nitriles radical conjugate addition ensues and gives the corresponding beta-functionalized aryl alkyl ketones in moderate to good yields (stereoselectively in the case of 3-methylene-2-norbornanone). Due to the mild reaction conditions the presence of various functional groups on the aromatic ring is tolerated (e.g. methyl, methoxy, chloro). The method can be applied to hetero-aromatic aldehydes whether electron-rich (e.g. thiophene-2-carbaldehyde) or electron-poor (e.g. pyridine-3-carbaldehyde).

Multifunctional receptor model for dioxin and related compound toxic action: possible thyroid hormone-responsive effector-linked site.

PubMed Central

McKinney, J D

1989-01-01

Molecular/theoretical modeling studies have revealed that thyroid hormones and toxic chlorinated aromatic hydrocarbons of environmental significance (for which dioxin or TCDD is the prototype) have similar structural properties that could be important in molecular recognition in biochemical systems. These molecular properties include a somewhat rigid, sterically accessible and polarizable aromatic ring and size-limited, hydrophobic lateral substituents, usually contained in opposite adjoining rings of a diphenyl compound. These molecular properties define the primary binding groups thought to be important in molecular recognition of both types of structures in biochemical systems. Similar molecular reactivities are supported by the demonstration of effective specific binding of thyroid hormones and chlorinated aromatic hydrocarbons with four different proteins, enzymes, or receptor preparations that are known or suspected to be involved in the expression of thyroid hormone activity. These binding interactions represent both aromatic-aromatic (stacking) and molecular cleft-type recognition processes. A multiple protein or multifunctional receptor-ligand binding mechanism model is proposed as a way of visualizing the details and possible role of both the stacking and cleft type molecular recognition factors in the expression of biological activity. The model suggests a means by which hormone-responsive effector-linked sites (possible protein-protein-DNA complexes) can maintain highly structurally specific control of hormone action. Finally, the model also provides a theoretical basis for the design and conduct of further biological experimentation on the molecular mechanism(s) of action of toxic chlorinated aromatic hydrocarbons and thyroid hormones. Images FIGURE 3. A FIGURE 3. B FIGURE 3. C FIGURE 3. D PMID:2551666

Catalysts for polyimide foams from aromatic isocyanates and aromatic dianhydrides. [flame retardant foams

NASA Technical Reports Server (NTRS)

Riccitiello, S. R.; Sawko, P. M.; Estrella, C. A. (Inventor)

1979-01-01

Polyimide foam products having greatly improved burn-through and flame-spread resistance are prepared by the reaction of aromatic polyisocyanates with aromatic dianhydrides in the presence of metallic salts of octoic acid. The salts, for example stannous octoate, ferric octoate and aluminum octoate, favor the formation of imide linkages at the expense of other possible reactions.

CHEMISTRY OF OXIDATION OF POLYCYCLIC AROMATIC HYDROCARBONS BY SOIL PSEUDOMONADS

PubMed Central

Rogoff, Martin H.

1962-01-01

Rogoff, Martin H. (U.S. Bureau of Mines, Pittsburgh, Pa.). Oxidation of polycyclic aromatic hydrocarbons by soil pseudomonads. J. Bacteriol. 83:998–1004. 1962.—Substitution of phenanthrene by a methyl group at the 9-carbon blocks oxidation of the compound by a resting-cell suspension of a phenanthrene-grown soil pseudomonad. When 2-methylphenanthrene is provided, the oxidation rate is considerably higher; 3-methylphenanthrene is oxidized at a rate intermediate between the other two, even though the methyl group is attached to a carbon directly involved in ring splitting. Cells grown on naphthalene or anthracene oxidize phenanthrene at a much lower rate than cells grown with phenanthrene or 2-methylnaphthalene as the source of carbon. Naphthalene-grown cells also absorb less phenanthrene from aqueous solution than do their phenanthrene-grown counterparts. The data are in keeping with the hypothesis that polynuclear aromatic hydrocarbons attach to the relevant bacterial enzymes at carbon-carbon bonds of high electron density (K regions; localized double bonds), and that the ring-splitting reactions then occur at other bonds on the substrate molecule. The actual bond that undergoes fission is determined by the electronic and steric configurations of the enzyme-substrate complex. When linearly arranged aromatic compounds such as naphthalene or anthracene are attacked, attachment to an enzyme and ring splitting may take place on the same ring; angular aromatic compounds such as phenanthrene afford attachment to an enzyme at a bond in a ring other than the one containing the ring-splitting site. PMID:14493381

Combining molecular docking and QSAR studies for modeling the anti-tyrosinase activity of aromatic heterocycle thiosemicarbazone analogues

NASA Astrophysics Data System (ADS)

Dong, Huanhuan; Liu, Jing; Liu, Xiaoru; Yu, Yanying; Cao, Shuwen

2018-01-01

A collection of thirty-six aromatic heterocycle thiosemicarbazone analogues presented a broad span of anti-tyrosinase activities were designed and obtained. A robust and reliable two-dimensional quantitative structure-activity relationship model, as evidenced by the high q2 and r2 values (0.848 and 0.893, respectively), was gained based on the analogues to predict the quantitative chemical-biological relationship and the new modifier direction. Inhibitory activities of the compounds were found to greatly depend on molecular shape and orbital energy. Substituents brought out large ovality and high highest-occupied molecular orbital energy values helped to improve the activity of these analogues. The molecular docking results provided visual evidence for QSAR analysis and inhibition mechanism. Based on these, two novel tyrosinase inhibitors O04 and O05 with predicted IC50 of 0.5384 and 0.8752 nM were designed and suggested for further research.

Role of aromatic interactions in amyloid formation by islet amyloid polypeptide.

PubMed

Tu, Ling-Hsien; Raleigh, Daniel P

2013-01-15

Aromatic-aromatic and aromatic-hydrophobic interactions have been proposed to play a role in amyloid formation by a range of polypeptides, including islet amyloid polypeptide (IAPP or amylin). IAPP is responsible for amyloid formation in patients with type 2 diabetes. The polypeptide is 37 residues long and contains three aromatic residues, Phe-15, Phe-23, and Tyr-37. The ability of all single aromatic to leucine mutants, all double aromatic to leucine mutants, and the triple leucine mutant to form amyloid were examined. Amyloid formation was almost twice as rapid for the F15L mutant as for the wild type but was almost 3-fold slower for the Y37L mutant and almost 2-fold slower for the F23L mutant. Amyloid fibrils formed from each of the single mutants were effective at seeding amyloid formation by wild-type IAPP, implying that the fibril structures are similar. The F15L/F23L double mutant has a larger effect than the F15L/Y37L double mutant on the rate of amyloid formation, even though a Y37L substitution has more drastic consequences in the wild-type background than does the F23L mutation, suggesting nonadditive effects between the different sites. The triple leucine mutant and the F23L/Y37L double mutant are the slowest to form amyloid. F15 has been proposed to make important contacts early in the aggregation pathway, but the data for the F15L mutant indicate that they are not optimal. A set of variants containing natural and unnatural amino acids at position 15, which were designed to conserve hydrophobicity, but alter α-helix and β-sheet propensity, were analyzed to determine the properties of this position that control the rate of amyloid formation. There is no correlation between β-sheet propensity at this position and the rate of amyloid formation, but there is a correlation with α-helical propensity.

Antioxidant effect of aromatic volatiles emitted by Lavandula dentata, Mentha spicata, and M. piperita on mouse subjected to low oxygen condition.

PubMed

Hu, Zenghui; Wang, Chunling; Shen, Hong; Zhang, Kezhong; Leng, Pingsheng

2017-12-01

This study aims to investigate the antioxidant effect of aromatic volatiles of three common aromatic plants, Lavandula dentata, Mentha spicata, and M. piperita. In this study, kunming mice subjected to low oxygen condition were treated with the volatiles emitted from these aromatic plants through inhalation administration. Then the blood cell counts, and the activities and gene expressions of antioxidant enzymes in different tissues were tested. The results showed that low oxygen increased the counts of red blood cells, white blood cells, and blood platelets of mice, and aromatic volatiles decreased their counts. Exposure to aromatic volatiles resulted in decreases in the malonaldehyde contents, and increases in the activities and gene expressions of superoxide dismutase, glutathione peroxidase, and catalase in different tissues under low oxygen. In addition, as the main component of aromatic volatiles, eucalyptol was the potential source that imparted positive antioxidant effect.

Enhancement of the ETS-10 titanosilicate activity in the shape-selective photocatalytic degradation of large aromatic molecules by controlled defect production.

PubMed

Llabrés I Xamena, Francesc X; Calza, Paola; Lamberti, Carlo; Prestipino, Carmelo; Damin, Alessandro; Bordiga, Silvia; Pelizzetti, Ezio; Zecchina, Adriano

2003-02-26

In recent times, it has been shown that the microporous ETS-10 titanosilicate can be used as a shape-selective photocatalyst for the decomposition of aromatic molecules (Chem. Commun. 2001, 2131). Its actual use on practical grounds is however discouraged by its too low activity, when compared with that of TiO(2) photocatalysts. In the present work, we show how an ad hoc mild treatment with HF enhances the activity of ETS-10 toward the photodegradation of large aromatic molecules that are unable to penetrate inside the zeolitic pores, such as 2,5-dichlorophenol, 2,4,5-trichlorophenol, 1,3,5-trihydroxybenzene, and 2,3-dihydroxynaphthalene (DHN). The photoactivity of the acid-treated materials is comparable or even greater than that of the nonselective TiO(2) catalyst. Moreover, the enhancement of the photoactivity is accompanied by a remarkable parallel increase of the shape selectivity, particularly toward DHN (k(DHN)/k(P) = 127, where P = phenol). A complete characterization (by means of X-ray diffraction, scanning electron microscopy, transmission electron microscopy, ultraviolet-visible spectroscopy, and X-ray aborption spectroscopy techniques) of a set of ETS-10 samples which have undergone a progressively severe HF treatment allows us to propose an explanation of the photocatalytic activity and selectivity of the modified materials.

Ionizable Side Chains at Catalytic Active Sites of Enzymes

PubMed Central

Jimenez-Morales, David; Liang, Jie

2012-01-01

Catalytic active sites of enzymes of known structure can be well defined by a modern program of computational geometry. The CASTp program was used to define and measure the volume of the catalytic active sites of 573 enzymes in the Catalytic Site Atlas database. The active sites are identified as catalytic because the amino acids they contain are known to participate in the chemical reaction catalyzed by the enzyme. Acid and base side chains are reliable markers of catalytic active sites. The catalytic active sites have 4 acid and 5 base side chains, in an average volume of 1072 Å3. The number density of acid side chains is 8.3 M (in chemical units); the number density of basic side chains is 10.6 M. The catalytic active site of these enzymes is an unusual electrostatic and steric environment in which side chains and reactants are crowded together in a mixture more like an ionic liquid than an ideal infinitely dilute solution. The electrostatics and crowding of reactants and side chains seems likely to be important for catalytic function. In three types of analogous ion channels, simulation of crowded charges accounts for the main properties of selectivity measured in a wide range of solutions and concentrations. It seems wise to use mathematics designed to study interacting complex fluids when making models of the catalytic active sites of enzymes. PMID:22484856

Removal of Intermediate Aromatic Halogenated DBPs by Activated Carbon Adsorption: A New Approach to Controlling Halogenated DBPs in Chlorinated Drinking Water.

PubMed

Jiang, Jingyi; Zhang, Xiangru; Zhu, Xiaohu; Li, Yu

2017-03-21

During chlorine disinfection of drinking water, chlorine may react with natural organic matter (NOM) and bromide ion in raw water to generate halogenated disinfection byproducts (DBPs). To mitigate adverse effects from DBP exposure, granular activated carbon (GAC) adsorption has been considered as one of the best available technologies for removing NOM (DBP precursor) in drinking water treatment. Recently, we have found that many aromatic halogenated DBPs form in chlorination, and they act as intermediate DBPs to decompose and form commonly known DBPs including trihalomethanes and haloacetic acids. In this work, we proposed a new approach to controlling drinking water halogenated DBPs by GAC adsorption of intermediate aromatic halogenated DBPs during chlorination, rather than by GAC adsorption of NOM prior to chlorination (i.e., traditional approach). Rapid small-scale column tests were used to simulate GAC adsorption in the new and traditional approaches. Significant reductions of aromatic halogenated DBPs were observed in the effluents with the new approach; the removals of total organic halogen, trihalomethanes, and haloacetic acids by the new approach always exceeded those by the traditional approach; and the effluents with the new approach were considerably less developmentally toxic than those with the traditional approach. Our findings indicate that the new approach is substantially more effective in controlling halogenated DBPs than the traditional approach.

PHOTOACTIVATED POLYCYCLIC AROMATIC HYDROCARBON TOXICITY IN MEDAKA (ORYZIAS LATIPES) EMBRYOS: RELEVANCE TO ENVIRONMENTAL RISK IN CONTAMINATED SITES

EPA Science Inventory

The hazard for photoactivated toxicity of polycyclic aromatic hydrocarbons (PAHs) has been clearly demonstrated; however, to our knowledge, the risk in contaminated systems has not been characterized. To address this question, a median lethal dose (LD50) for fluoranthene photoa...

Polynuclear aromatic hydrocarbons for fullerene synthesis in flames

DOEpatents

Alford, J. Michael; Diener, Michael D.

2006-12-19

This invention provides improved methods for combustion synthesis of carbon nanomaterials, including fullerenes, employing multiple-ring aromatic hydrocarbon fuels selected for high carbon conversion to extractable fullerenes. The multiple-ring aromatic hydrocarbon fuels include those that contain polynuclear aromatic hydrocarbons. More specifically, multiple-ring aromatic hydrocarbon fuels contain a substantial amount of indene, methylnapthalenes or mixtures thereof. Coal tar and petroleum distillate fractions provide low cost hydrocarbon fuels containing polynuclear aromatic hydrocarbons, including without limitation, indene, methylnapthalenes or mixtures thereof.

Characterization of elemental and polycyclic aromatic hydrocarbon compositions of urban air in Brisbane

NASA Astrophysics Data System (ADS)

Lim, McKenzie C. H.; Ayoko, Godwin A.; Morawska, Lidia

Characterization of the elemental and polycyclic aromatic hydrocarbons (PAHs) compositions of urban air was undertaken at three major sites in Brisbane, Australia. 17 elements and 16 US EPA priority PAHs were quantified at the sites. The most commonly detected elements in the TSP and PM 2.5 fractions were Al, Cd, Co, Cr, Cu, Fe, Mn, Mo, Si, Sn, Sr and Zn. Compared to the two other sites, PM 2.5 was found to contain higher concentrations of Zr, Mo, V, Al, Mn and Sr at the Queensland University of Technology (QUT) site. In contrast, the Woolloongabba sampling site, which was highly influenced by the vehicular emission and local industrial activities, has higher concentrations of Co, Sn, Cu, Zn and Mg while ANZ site has significantly lower concentration levels of most elements than the other sites; possibly due to the shielding effect of the nearby bush and forest. NAP, PHE, ANT, FLT, PYR and CRY were the most widespread PAHs found in all sites. But only QUT and Woolloongabba bus platform sites had detectable levels of the most carcinogenic US EPA PAH, BAP. The multi-criteria decision making procedures, Preference Ranking Organisation Method for Enrichment Evaluation (PROMETHEE) and Geometrical Analysis for Interactive Aid (GAIA) were used to rank the air samples and to identify the sources of the pollutants. Thus Woolloongabba bus platform was ranked as the most polluted site on the basis of the elemental and PAH compositions of its air samples while Woolloongabba bus platform and QUT sites were ranked as the worst polluted sites in terms of PAHs and PM 2.5 elemental contents, respectively.

Discriminative structural approaches for enzyme active-site prediction.

PubMed

Kato, Tsuyoshi; Nagano, Nozomi

2011-02-15

Predicting enzyme active-sites in proteins is an important issue not only for protein sciences but also for a variety of practical applications such as drug design. Because enzyme reaction mechanisms are based on the local structures of enzyme active-sites, various template-based methods that compare local structures in proteins have been developed to date. In comparing such local sites, a simple measurement, RMSD, has been used so far. This paper introduces new machine learning algorithms that refine the similarity/deviation for comparison of local structures. The similarity/deviation is applied to two types of applications, single template analysis and multiple template analysis. In the single template analysis, a single template is used as a query to search proteins for active sites, whereas a protein structure is examined as a query to discover the possible active-sites using a set of templates in the multiple template analysis. This paper experimentally illustrates that the machine learning algorithms effectively improve the similarity/deviation measurements for both the analyses.

Characterization and engineering of a plastic-degrading aromatic polyesterase

PubMed Central

Austin, Harry P.; Allen, Mark D.; Rorrer, Nicholas A.; Kearns, Fiona L.; Silveira, Rodrigo L.; Pollard, Benjamin C.; Dominick, Graham; El Omari, Kamel; Mykhaylyk, Vitaliy; Michener, William E.; Amore, Antonella; Skaf, Munir S.; Crowley, Michael F.; Thorne, Alan W.; Johnson, Christopher W.; Woodcock, H. Lee

2018-01-01

Poly(ethylene terephthalate) (PET) is one of the most abundantly produced synthetic polymers and is accumulating in the environment at a staggering rate as discarded packaging and textiles. The properties that make PET so useful also endow it with an alarming resistance to biodegradation, likely lasting centuries in the environment. Our collective reliance on PET and other plastics means that this buildup will continue unless solutions are found. Recently, a newly discovered bacterium, Ideonella sakaiensis 201-F6, was shown to exhibit the rare ability to grow on PET as a major carbon and energy source. Central to its PET biodegradation capability is a secreted PETase (PET-digesting enzyme). Here, we present a 0.92 Å resolution X-ray crystal structure of PETase, which reveals features common to both cutinases and lipases. PETase retains the ancestral α/β-hydrolase fold but exhibits a more open active-site cleft than homologous cutinases. By narrowing the binding cleft via mutation of two active-site residues to conserved amino acids in cutinases, we surprisingly observe improved PET degradation, suggesting that PETase is not fully optimized for crystalline PET degradation, despite presumably evolving in a PET-rich environment. Additionally, we show that PETase degrades another semiaromatic polyester, polyethylene-2,5-furandicarboxylate (PEF), which is an emerging, bioderived PET replacement with improved barrier properties. In contrast, PETase does not degrade aliphatic polyesters, suggesting that it is generally an aromatic polyesterase. These findings suggest that additional protein engineering to increase PETase performance is realistic and highlight the need for further developments of structure/activity relationships for biodegradation of synthetic polyesters. PMID:29666242

Characterization and engineering of a plastic-degrading aromatic polyesterase.

PubMed

Austin, Harry P; Allen, Mark D; Donohoe, Bryon S; Rorrer, Nicholas A; Kearns, Fiona L; Silveira, Rodrigo L; Pollard, Benjamin C; Dominick, Graham; Duman, Ramona; El Omari, Kamel; Mykhaylyk, Vitaliy; Wagner, Armin; Michener, William E; Amore, Antonella; Skaf, Munir S; Crowley, Michael F; Thorne, Alan W; Johnson, Christopher W; Woodcock, H Lee; McGeehan, John E; Beckham, Gregg T

2018-05-08

Poly(ethylene terephthalate) (PET) is one of the most abundantly produced synthetic polymers and is accumulating in the environment at a staggering rate as discarded packaging and textiles. The properties that make PET so useful also endow it with an alarming resistance to biodegradation, likely lasting centuries in the environment. Our collective reliance on PET and other plastics means that this buildup will continue unless solutions are found. Recently, a newly discovered bacterium, Ideonella sakaiensis 201-F6, was shown to exhibit the rare ability to grow on PET as a major carbon and energy source. Central to its PET biodegradation capability is a secreted PETase (PET-digesting enzyme). Here, we present a 0.92 Å resolution X-ray crystal structure of PETase, which reveals features common to both cutinases and lipases. PETase retains the ancestral α/β-hydrolase fold but exhibits a more open active-site cleft than homologous cutinases. By narrowing the binding cleft via mutation of two active-site residues to conserved amino acids in cutinases, we surprisingly observe improved PET degradation, suggesting that PETase is not fully optimized for crystalline PET degradation, despite presumably evolving in a PET-rich environment. Additionally, we show that PETase degrades another semiaromatic polyester, polyethylene-2,5-furandicarboxylate (PEF), which is an emerging, bioderived PET replacement with improved barrier properties. In contrast, PETase does not degrade aliphatic polyesters, suggesting that it is generally an aromatic polyesterase. These findings suggest that additional protein engineering to increase PETase performance is realistic and highlight the need for further developments of structure/activity relationships for biodegradation of synthetic polyesters. Copyright © 2018 the Author(s). Published by PNAS.

Characterization and engineering of a plastic-degrading aromatic polyesterase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Austin, Harry P.; Allen, Mark D.; Donohoe, Bryon S.

Poly(ethylene terephthalate) (PET) is one of the most abundantly produced synthetic polymers and is accumulating in the environment at a staggering rate as discarded packaging and textiles. The properties that make PET so useful also endow it with an alarming resistance to biodegradation, likely lasting centuries in the environment. Our collective reliance on PET and other plastics means that this buildup will continue unless solutions are found. Recently, a newly discovered bacterium, Ideonella sakaiensis 201-F6, was shown to exhibit the rare ability to grow on PET as a major carbon and energy source. Central to its PET biodegradation capability ismore » a secreted PETase (PET-digesting enzyme). Here, we present a 0.92 A resolution X-ray crystal structure of PETase, which reveals features common to both cutinases and lipases. PETase retains the ancestral a/..beta..-hydrolase fold but exhibits a more open active-site cleft than homologous cutinases. By narrowing the binding cleft via mutation of two active-site residues to conserved amino acids in cutinases, we surprisingly observe improved PET degradation, suggesting that PETase is not fully optimized for crystalline PET degradation, despite presumably evolving in a PET-rich environment. Additionally, we show that PETase degrades another semiaromatic polyester, polyethylene-2,5-furandicarboxylate (PEF), which is an emerging, bioderived PET replacement with improved barrier properties. In contrast, PETase does not degrade aliphatic polyesters, suggesting that it is generally an aromatic polyesterase. These findings suggest that additional protein engineering to increase PETase performance is realistic and highlight the need for further developments of structure/activity relationships for biodegradation of synthetic polyesters.« less

Characterization and engineering of a plastic-degrading aromatic polyesterase

DOE PAGES

Austin, Harry P.; Allen, Mark D.; Donohoe, Bryon S.; ...

2018-04-17

Poly(ethylene terephthalate) (PET) is one of the most abundantly produced synthetic polymers and is accumulating in the environment at a staggering rate as discarded packaging and textiles. The properties that make PET so useful also endow it with an alarming resistance to biodegradation, likely lasting centuries in the environment. Our collective reliance on PET and other plastics means that this buildup will continue unless solutions are found. Recently, a newly discovered bacterium, Ideonella sakaiensis 201-F6, was shown to exhibit the rare ability to grow on PET as a major carbon and energy source. Central to its PET biodegradation capability ismore » a secreted PETase (PET-digesting enzyme). Here, we present a 0.92 A resolution X-ray crystal structure of PETase, which reveals features common to both cutinases and lipases. PETase retains the ancestral a/..beta..-hydrolase fold but exhibits a more open active-site cleft than homologous cutinases. By narrowing the binding cleft via mutation of two active-site residues to conserved amino acids in cutinases, we surprisingly observe improved PET degradation, suggesting that PETase is not fully optimized for crystalline PET degradation, despite presumably evolving in a PET-rich environment. Additionally, we show that PETase degrades another semiaromatic polyester, polyethylene-2,5-furandicarboxylate (PEF), which is an emerging, bioderived PET replacement with improved barrier properties. In contrast, PETase does not degrade aliphatic polyesters, suggesting that it is generally an aromatic polyesterase. These findings suggest that additional protein engineering to increase PETase performance is realistic and highlight the need for further developments of structure/activity relationships for biodegradation of synthetic polyesters.« less

Emissions of Polycyclic Aromatic Hydrocarbons from Natural Gas Extraction into Air.

PubMed

Paulik, L Blair; Donald, Carey E; Smith, Brian W; Tidwell, Lane G; Hobbie, Kevin A; Kincl, Laurel; Haynes, Erin N; Anderson, Kim A

2016-07-19

Natural gas extraction, often referred to as "fracking", has increased rapidly in the United States in recent years. To address potential health impacts, passive air samplers were deployed in a rural community heavily affected by the natural gas boom. Samplers were analyzed for 62 polycyclic aromatic hydrocarbons (PAHs). Results were grouped based on distance from each sampler to the nearest active well. Levels of benzo[a]pyrene, phenanthrene, and carcinogenic potency of PAH mixtures were highest when samplers were closest to active wells. PAH levels closest to natural gas activity were comparable to levels previously reported in rural areas in winter. Sourcing ratios indicated that PAHs were predominantly petrogenic, suggesting that PAH levels were influenced by direct releases from the earth. Quantitative human health risk assessment estimated the excess lifetime cancer risks associated with exposure to the measured PAHs. At sites closest to active wells, the risk estimated for maximum residential exposure was 0.04 in a million, which is below the U.S. Environmental Protection Agency's acceptable risk level. Overall, risk estimates decreased 30% when comparing results from samplers closest to active wells to those farthest from them. This work suggests that natural gas extraction is contributing PAHs to the air, at levels that would not be expected to increase cancer risk.

Pseudomonads biodegradation of aromatic compounds in oil sands process-affected water.

PubMed

Zhang, Yanyan; McPhedran, Kerry N; Gamal El-Din, Mohamed

2015-07-15

Aromatic naphthenic acids (NAs) have been shown to be more toxic than the classical NAs found in oil sands process-affected water (OSPW). To reduce this toxicity, Pseudomonas fluorescens and Pseudomonas putida were used to determine their ability to biodegrade aromatic compounds including treatments considering the impacts of external carbon and iron addition. Results showed that with added carbon P. fluorescens and P. putida have the capability of biodegrading these aromatics. In the presence of external carbon, gene expression of a functional PAH-ring hydroxylating dioxygenase (PAH-RHDα) was determined through reverse transcription real-time PCR, suggesting active degradation of OSPW aromatic compounds. Although no significant classical NAs removal was observed during this process, toxicity was reduced by 49.3% under optimal conditions. OSPW toxicity was eliminated with the combination of ozonation at a dose of 80 mg/L followed by biodegradation, indicating that it is a promising combined OSPW treatment approach for the safe discharge to the aquatic environment. Copyright © 2015 Elsevier B.V. All rights reserved.

Binding of tetramethylammonium to polyether side-chained aromatic hosts. Evaluation of the binding contribution from ether oxygen donors.

PubMed

Bartoli, Sandra; De Nicola, Gina; Roelens, Stefano

2003-10-17

A set of macrocyclic and open-chain aromatic ligands endowed with polyether side chains has been prepared to assess the contribution of ether oxygen donors to the binding of tetramethylammonium (TMA), a cation believed incapable of interacting with oxygen donors. The open-chain hosts consisted of an aromatic binding site and side chains possessing a variable number of ether oxygen donors; the macrocyclic ligands were based on the structure of a previously investigated host, the dimeric cyclophane 1,4-xylylene-1,4-phenylene diacetate (DXPDA), implemented with polyether-type side chains in the backbone. Association to tetramethylammonium picrate (TMAP) was measured in CDCl(3) at T = 296 K by (1)H NMR titrations. Results confirm that the main contribution to the binding of TMA comes from the cation-pi interaction established with the aromatic binding sites, but they unequivocally show that polyether chains participate with cooperative contributions, although of markedly smaller entity. Water is also bound, but the two guests interact with aromatic rings and oxygen donors in an essentially noncompetitive way. An improved procedure for the preparation of cyclophanic tetraester derivatives has been developed that conveniently recycles the oligomeric ester byproducts formed in the one-pot cyclization reaction. An alternative entry to benzylic diketones has also been provided that makes use of a low-order cyanocuprate reagent to prepare in fair yields a class of compounds otherwise uneasily accessible.

Ionic liquid mediated synthesis and molecular docking study of novel aromatic embedded Schiff bases as potent cholinesterase inhibitors.

PubMed

Abd Razik, Basma M; Osman, Hasnah; Basiri, Alireza; Salhin, Abdussalam; Kia, Yalda; Ezzat, Mohammed Oday; Murugaiyah, Vikneswaran

2014-12-01

Novel aromatic embedded Schiff bases have been synthesized in ionic liquid [bmim]Br and evaluated in vitro for their acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) enzymes inhibitory activities. Among the newly synthesized compounds, 5f, 5h and 7j displayed higher AChE enzyme inhibitory activities than standard drug, galanthamine, with IC50 values of 1.88, 2.05 and 2.03μM, respectively. Interestingly, all the compounds except for compound 5c displayed higher BChE inhibitories than standard with IC50 values ranging from 3.49 to 19.86μM. Molecular docking analysis for 5f and 7j possessing the most potent AChE and BChE inhibitory activities, disclosed their binding interaction templates to the active site of AChE and BChE enzymes, respectively. Copyright © 2014 Elsevier Inc. All rights reserved.

Ultrahigh Molecular Weight Aromatic Siloxane Polymers

NASA Technical Reports Server (NTRS)

Ludwick, L. M.

1983-01-01

Silphenylene-siloxane polymers can be prepared by a condensation reaction of a diol 1,4-bis(hydroxydimethylsilyl)benzene and a silane bis(dimethylamino)dimethylsilane. Using a stepwise condensation technique, a polymer (R=CH3) with a molecular weight in excess of 1.0 x 1 million has been produced. The polymer exhibits increased thermal stability, compared to a methyl siloxane polymer without the aromatic phenyl ring in the backbone. The use of bis(dimethylamino)methylvinylsilane should allow for ready crosslinking at the vinyl sites (R=-CH=CH2) introduced into the backbone. However, under the conditions of the reaction system a high molecular weight polymer was not obtained or the polymer underwent a crosslinking process during the synthesis.

Ionizable side chains at catalytic active sites of enzymes.

PubMed

Jimenez-Morales, David; Liang, Jie; Eisenberg, Bob

2012-05-01

Catalytic active sites of enzymes of known structure can be well defined by a modern program of computational geometry. The CASTp program was used to define and measure the volume of the catalytic active sites of 573 enzymes in the Catalytic Site Atlas database. The active sites are identified as catalytic because the amino acids they contain are known to participate in the chemical reaction catalyzed by the enzyme. Acid and base side chains are reliable markers of catalytic active sites. The catalytic active sites have 4 acid and 5 base side chains, in an average volume of 1,072 Å(3). The number density of acid side chains is 8.3 M (in chemical units); the number density of basic side chains is 10.6 M. The catalytic active site of these enzymes is an unusual electrostatic and steric environment in which side chains and reactants are crowded together in a mixture more like an ionic liquid than an ideal infinitely dilute solution. The electrostatics and crowding of reactants and side chains seems likely to be important for catalytic function. In three types of analogous ion channels, simulation of crowded charges accounts for the main properties of selectivity measured in a wide range of solutions and concentrations. It seems wise to use mathematics designed to study interacting complex fluids when making models of the catalytic active sites of enzymes.

Electronic Structure Principles and Aromaticity

ERIC Educational Resources Information Center

Chattaraj, P. K.; Sarkar, U.; Roy, D. R.

2007-01-01

The relationship between aromaticity and stability in molecules on the basis of quantities such as hardness and electrophilicity is explored. The findings reveal that aromatic molecules are less energetic, harder, less polarizable, and less electrophilic as compared to antiaromatic molecules, as expected from the electronic structure principles.

Patterns and sources of particle-phase aliphatic and polycyclic aromatic hydrocarbons in urban and rural sites of western Greece

NASA Astrophysics Data System (ADS)

Kalaitzoglou, Maria; Terzi, Eleni; Samara, Constantini

Particle-bound aliphatic and polycyclic aromatic hydrocarbons (AHs and PAHs, respectively) were determined in the ambient air of the Eordea basin, in western Greece, where intensive coal burning for power generation takes place. Thirteen PAHs, n-alkanes (C 14-C 35), hopanes, and isoprenoid hydrocarbons (pristane and phytane) were determined in the total suspended particles collected from the atmosphere of four sites within the basin receiving potential impacts from various sources, such as fly ash, coal mining, automobile traffic, domestic heating, and agricultural or refuse burning. The same organic species were also determined in the fly ash generated in power stations, and in particulate emissions from open burning of biomass (dry corn leaves) and refuse burning. Organic particle sources were resolved using concentration diagnostic ratios and factor analysis (FA). A multivariate statistical receptor model (Absolute Principal Component Analysis, APCA) was finally employed to estimate the contribution of identified sources to the measured concentrations of organic pollutants. Four major sources for ambient PAHs and AHs were identified displaying variable contribution in different sites: (a) fossil fuel combustion, (b) biogenic emissions, (c) refuse burning, and (d) oil residues. Fuel combustion was the major source of ambient PAHs and an important source of n-alkanes in the range C 21-C 28. Oil residues were found to be the major source of low molecular weight n-alkanes (particularly the C 14-C 16), and an important source of pristane, phytane and UCM. Biogenic sources were primarily responsible for the high molecular weight n-alkanes explaining almost the entire concentration levels of homologues >C 32. Biomass burning was particularly important for the C 23-C 26n-alkanes. Despite the vicinity of certain sampling sites to power stations, coal fly ash was not identifiable as a source for ambient PAHs and AHs.

AROMATIC AND POLYCYCLIC AROMATIC HYDROCARBON FORMATION IN A LAMINAR PREMIXED N-BUTANE FLAME. (R825412)

EPA Science Inventory

Abstract

Experimental and detailed chemical kinetic modeling work has been performed to investigate aromatic and polycyclic aromatic hydrocarbon (PAH) formation pathways in a premixed, rich, sooting, n-butane_¯oxygen_¯argon burner s...

Airborne Exposures to Polycyclic Aromatic Compounds Among Workers in Asphalt Roofing Manufacturing Facilities.

PubMed

Trumbore, David C; Osborn, Linda V; Johnson, Kathleen A; Fayerweather, William E

2015-01-01

We studied exposure of 151 workers to polycyclic aromatic compounds and asphalt emissions during the manufacturing of asphalt roofing products-including 64 workers from 10 asphalt plants producing oxidized, straight-run, cutback, and wax- or polymer-modified asphalts, and 87 workers from 11 roofing plants producing asphalt shingles and granulated roll roofing. The facilities were located throughout the United States and used asphalt from many refiners and crude oils. This article helps fill a gap in exposure data for asphalt roofing manufacturing workers by using a fluorescence technique that targets biologically active 4-6 ring polycyclic aromatic compounds and is strongly correlated with carcinogenic activity in animal studies. Worker exposures to polycyclic aromatic compounds were compared between manufacturing plants, at different temperatures and using different raw materials, and to important external benchmarks. High levels of fine limestone particulate in the plant air during roofing manufacturing increased polycyclic aromatic compound exposure, resulting in the hypothesis that the particulate brought adsorbed polycyclic aromatic compounds to the worker breathing zone. Elevated asphalt temperatures increased exposures during the pouring of asphalt. Co-exposures in these workplaces which act as confounders for both the measurement of total organic matter and fluorescence were detected and their influence discussed. Exposures to polycyclic aromatic compounds in asphalt roofing manufacturing facilities were lower than or similar to those reported in hot-mix paving application studies, and much below those reported in studies of hot application of built-up roofing asphalt. These relatively low exposures in manufacturing are primarily attributed to air emission controls in the facilities, and the relatively moderate temperatures, compared to built-up roofing, used in these facilities for oxidized asphalt. The exposure to polycyclic aromatic compounds was a very

The Aromaticity of Pericyclic Reaction Transition States

ERIC Educational Resources Information Center

Rzepa, Henry S.

2007-01-01

An approach is presented that starts from two fundamental concepts in organic chemistry, chirality and aromaticity, and combines them into a simple rule for stating selection rules for pericyclic reactions in terms of achiral Huckel-aromatic and chiral Mobius-aromatic transition states. This is illustrated using an example that leads to apparent…

Simultaneous removal of sulfur dioxide and polycyclic aromatic hydrocarbons from incineration flue gas using activated carbon fibers.

PubMed

Liu, Zhen-Shu; Li, Wen-Kai; Hung, Ming-Jui

2014-09-01

Incineration flue gas contains polycyclic aromatic hydrocarbons (PAHs) and sulfur dioxide (SO2). The effects of SO2 concentration (0, 350, 750, and 1000 ppm), reaction temperature (160, 200, and 280 degrees C), and the type of activated carbon fibers (ACFs) on the removal of SO2 and PAHs by ACFs were examined in this study. A fluidized bed incinerator was used to simulate practical incineration flue gas. It was found that the presence of SO2 in the incineration flue gas could drastically decrease removal of PAHs because of competitive adsorption. The effect of rise in the reaction temperature from 160 to 280 degrees C on removal of PAHs was greater than that on SO2 removal at an SO2 concentration of 750 ppm. Among the three ACFs studied, ACF-B, with the highest microporous volume, highest O content, and the tightest structure, was the best adsorbent for removing SO2 and PAHs when these gases coexisted in the incineration flue gas. Implications: Simultaneous adsorption of sulfur dioxide (SO2) and polycyclic aromatic hydrocarbons (PAHs) emitted from incineration flue gas onto activated carbon fibers (ACFs) meant to devise a new technique showed that the presence of SO2 in the incineration flue gas leads to a drastic decrease in removal of PAHs because of competitive adsorption. Reaction temperature had a greater influence on PAHs removal than on SO2 removal. ACF-B, with the highest microporous volume, highest O content, and tightest structure among the three studied ACFs, was found to be the best adsorbent for removing SO2 and PAHs.

Sulphur Atoms from Methionines Interacting with Aromatic Residues Are Less Prone to Oxidation

PubMed Central

Aledo, Juan C.; Cantón, Francisco R.; Veredas, Francisco J.

2015-01-01

Methionine residues exhibit different degrees of susceptibility to oxidation. Although solvent accessibility is a relevant factor, oxidation at particular sites cannot be unequivocally explained by accessibility alone. To explore other possible structural determinants, we assembled different sets of oxidation-sensitive and oxidation-resistant methionines contained in human proteins. Comparisons of the proteins containing oxidized methionines with all proteins in the human proteome led to the conclusion that the former exhibit a significantly higher mean value of methionine content than the latter. Within a given protein, an examination of the sequence surrounding the non-oxidized methionine revealed a preference for neighbouring tyrosine and tryptophan residues, but not for phenylalanine residues. However, because the interaction between sulphur atoms and aromatic residues has been reported to be important for the stabilization of protein structure, we carried out an analysis of the spatial interatomic distances between methionines and aromatic residues, including phenylalanine. The results of these analyses uncovered a new determinant for methionine oxidation: the S-aromatic motif, which decreases the reactivity of the involved sulphur towards oxidants. PMID:26597773

Four Aromatic Sulfates with an Inhibitory Effect against HCV NS3 Helicase from the Crinoid Alloeocomatella polycladia.

PubMed

Hermawan, Idam; Furuta, Atsushi; Higashi, Masahiro; Fujita, Yoshihisa; Akimitsu, Nobuyoshi; Yamashita, Atsuya; Moriishi, Kohji; Tsuneda, Satoshi; Tani, Hidenori; Nakakoshi, Masamichi; Tsubuki, Masayoshi; Sekiguchi, Yuji; Noda, Naohiro; Tanaka, Junichi

2017-04-11

Bioassay-guided separation of a lipophilic extract of the crinoid Alloeocomatella polycladia , inhibiting the activity of HCV NS3 helicase, yielded two groups of molecules: cholesterol sulfate and four new aromatic sulfates 1 - 4 . The structures of the aromatics were elucidated by spectroscopic analysis in addition to theoretical studies. The aromatic sulfates 1 - 4 showed moderate inhibition against NS3 helicase with IC 50 values of 71, 95, 7, and 5 μM, respectively.

Metal active site elasticity linked to activation of homocysteine in methionine synthases

DOE Office of Scientific and Technical Information (OSTI.GOV)

Koutmos, Markos; Pejchal, Robert; Bomer, Theresa M.

2008-04-02

Enzymes possessing catalytic zinc centers perform a variety of fundamental processes in nature, including methyl transfer to thiols. Cobalamin-independent (MetE) and cobalamin-dependent (MetH) methionine synthases are two such enzyme families. Although they perform the same net reaction, transfer of a methyl group from methyltetrahydrofolate to homocysteine (Hcy) to form methionine, they display markedly different catalytic strategies, modular organization, and active site zinc centers. Here we report crystal structures of zinc-replete MetE and MetH, both in the presence and absence of Hcy. Structural investigation of the catalytic zinc sites of these two methyltransferases reveals an unexpected inversion of zinc geometry uponmore » binding of Hcy and displacement of an endogenous ligand in both enzymes. In both cases a significant movement of the zinc relative to the protein scaffold accompanies inversion. These structures provide new information on the activation of thiols by zinc-containing enzymes and have led us to propose a paradigm for the mechanism of action of the catalytic zinc sites in these and related methyltransferases. Specifically, zinc is mobile in the active sites of MetE and MetH, and its dynamic nature helps facilitate the active site conformational changes necessary for thiol activation and methyl transfer.« less

Trimerization of aromatic nitriles

NASA Technical Reports Server (NTRS)

Hsu, L. C. (Inventor)

1977-01-01

Triazine compounds and cross-linked polymer compositions were made by heating aromatic nitriles to a temperature in the range of about 100 C to about 700 C, in the presence of a catalyst or mixture of catalysts. Aromatic nitrile-modified (terminated and/or appended) imide, benzimidazole, imidazopyrrolone, quinoxaline, and other condensation type prepolymers or their precopolymers were made which were trimerized with or without a filler by the aforementioned catalytic trimerization process.

Nicotinamide Cofactors Suppress Active-Site Labeling of Aldehyde Dehydrogenases.

PubMed

Stiti, Naim; Chandrasekar, Balakumaran; Strubl, Laura; Mohammed, Shabaz; Bartels, Dorothea; van der Hoorn, Renier A L

2016-06-17

Active site labeling by (re)activity-based probes is a powerful chemical proteomic tool to globally map active sites in native proteomes without using substrates. Active site labeling is usually taken as a readout for the active state of the enzyme because labeling reflects the availability and reactivity of active sites, which are hallmarks for enzyme activities. Here, we show that this relationship holds tightly, but we also reveal an important exception to this rule. Labeling of Arabidopsis ALDH3H1 with a chloroacetamide probe occurs at the catalytic Cys, and labeling is suppressed upon nitrosylation and oxidation, and upon treatment with other Cys modifiers. These experiments display a consistent and strong correlation between active site labeling and enzymatic activity. Surprisingly, however, labeling is suppressed by the cofactor NAD(+), and this property is shared with other members of the ALDH superfamily and also detected for unrelated GAPDH enzymes with an unrelated hydantoin-based probe in crude extracts of plant cell cultures. Suppression requires cofactor binding to its binding pocket. Labeling is also suppressed by ALDH modulators that bind at the substrate entrance tunnel, confirming that labeling occurs through the substrate-binding cavity. Our data indicate that cofactor binding adjusts the catalytic Cys into a conformation that reduces the reactivity toward chloroacetamide probes.

Complexation of C60 fullerene with aromatic drugs.

PubMed

Evstigneev, Maxim P; Buchelnikov, Anatoly S; Voronin, Dmitry P; Rubin, Yuriy V; Belous, Leonid F; Prylutskyy, Yuriy I; Ritter, Uwe

2013-02-25

The contributions of various physical factors to the energetics of complexation of aromatic drug molecules with C(60) fullerene are investigated in terms of the calculated magnitudes of equilibrium complexation constants and the components of the net Gibbs free energy. Models of complexation are developed taking into account the polydisperse nature of fullerene solutions in terms of the continuous or discrete (fractal) aggregation of C(60) molecules. Analysis of the energetics has shown that stabilization of the ligand-fullerene complexes in aqueous solution is mainly determined by intermolecular van der Waals interactions and, to lesser extent, by hydrophobic interactions. The results provide a physicochemical basis for a potentially new biotechnological application of fullerenes as modulators of biological activity of aromatic drugs. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

COMPARISON OF IMMUNOASSAY AND GAS CHROMATOGRAPHY/MASS SPECTROMETRY FOR MEASUREMENT OF POLYCYCLIC AROMATIC HYDROCARBONS IN CONTAMINATED SOIL

EPA Science Inventory

Polycyclic aromatic hydrocarbons (PAHs) are frequently encountered in the environment and may pose health concerns due to their carcinogenicity. A commercial enzyme-linked immunosorbent assay (ELISA), was evaluated as a screening method for monitoring PAHs at contaminated site...

Quantum mechanical design of enzyme active sites.

PubMed

Zhang, Xiyun; DeChancie, Jason; Gunaydin, Hakan; Chowdry, Arnab B; Clemente, Fernando R; Smith, Adam J T; Handel, T M; Houk, K N

2008-02-01

The design of active sites has been carried out using quantum mechanical calculations to predict the rate-determining transition state of a desired reaction in presence of the optimal arrangement of catalytic functional groups (theozyme). Eleven versatile reaction targets were chosen, including hydrolysis, dehydration, isomerization, aldol, and Diels-Alder reactions. For each of the targets, the predicted mechanism and the rate-determining transition state (TS) of the uncatalyzed reaction in water is presented. For the rate-determining TS, a catalytic site was designed using naturalistic catalytic units followed by an estimation of the rate acceleration provided by a reoptimization of the catalytic site. Finally, the geometries of the sites were compared to the X-ray structures of related natural enzymes. Recent advances in computational algorithms and power, coupled with successes in computational protein design, have provided a powerful context for undertaking such an endeavor. We propose that theozymes are excellent candidates to serve as the active site models for design processes.

Anti-tubercular activity of eleven aromatic and medicinal plants occurring in Colombia.

PubMed

Bueno-Sánchez, Juan Gabriel; Martínez-Morales, Jairo René; Stashenko, Elena E; Ribón, Wellman

2009-03-01

Human tuberculosis is a contagious-infectious disease mainly caused by Mycobacterium tuberculosis. Although regimens exist for treating tuberculosis, they are far from ideal. Development of effective strategies for treatment of human tuberculosis has posed a challenge, considering the increase in infections associated with the human immunodeficiency virus and immunocompromised patients. Essential oils--volatile, aromatic oil extracts from plants--have been used in traditional treatment of many diseases; however careful investigation of these oils has not been undertaken with respect to treatments of tuberculosis. The in vitro antitubercular activity of essential oils from 11 medicinal plants grown in Colombia were assessed for efficacy as new medications (phytomedicines) for treatment of M. tuberculosis H37Rv. Essential oil extraction and analysis were performed as described Stashenko et al. (2004). Minimal inhibitory concentrations were determined by a colorimetric macrodilution method, following the protocol described by Abate et al. (1998). Isoniazide and rifampin were used as control treatments. Bactericidal and bacteriostatic activity was measured using the method developed by the Clinical and Laboratory Standards Institute consigned in the M26-A protocol. Essential oils from Achyrocline alata and Swinglea glutinosa were the most active with minimal inhibitory concentrations of 62.5 +/- 0.1 and 100 +/- 36 microg ml(-1), respectively. Carvacrol, thymol, p-cymene, 1,8-cineole, limonene, and beta-pinene were the major components, most often identified in the 11 plant extracts of essential oils. Time-kill curve assays demonstrated the bacteriostatic activity of these essential oils. The essential oils from A. alata and S. glutinosa plants, and the components identified therein, are candidates as potential phytotherapeutic agents for human tuberculosis control.

Four Aromatic Sulfates with an Inhibitory Effect against HCV NS3 Helicase from the Crinoid Alloeocomatella polycladia

PubMed Central

Hermawan, Idam; Furuta, Atsushi; Higashi, Masahiro; Fujita, Yoshihisa; Akimitsu, Nobuyoshi; Yamashita, Atsuya; Moriishi, Kohji; Tsuneda, Satoshi; Tani, Hidenori; Nakakoshi, Masamichi; Tsubuki, Masayoshi; Sekiguchi, Yuji; Noda, Naohiro; Tanaka, Junichi

2017-01-01

Bioassay-guided separation of a lipophilic extract of the crinoid Alloeocomatella polycladia, inhibiting the activity of HCV NS3 helicase, yielded two groups of molecules: cholesterol sulfate and four new aromatic sulfates 1–4. The structures of the aromatics were elucidated by spectroscopic analysis in addition to theoretical studies. The aromatic sulfates 1–4 showed moderate inhibition against NS3 helicase with IC50 values of 71, 95, 7, and 5 μM, respectively. PMID:28398249

THE PHOTOTOXICITY OF POLYCYCLIC AROMATIC HYDROCARBONS

EPA Science Inventory

The U.S. Environmental Protection Agency (EPA) continues to be interested in developing methods for the detection of polycyclic aromatic hydrocarbons (PAHS) in the environment. Polycyclic aromatic hydrocarbons (PAHS) are common contaminants in our environment. Being major product...

Aryl hydrocarbon receptor-mediated activity of atmospheric particulate matter from an urban and a rural site in Switzerland

NASA Astrophysics Data System (ADS)

Wenger, Daniela; Gerecke, Andreas C.; Heeb, Norbert V.; Hueglin, Christoph; Seiler, Cornelia; Haag, Regula; Naegeli, Hanspeter; Zenobi, Renato

Atmospheric particulate matter (PM) is an air-suspended mixture of solid and liquid particles that vary in size, shape, and chemical composition. Long-term exposure to elevated concentrations of fine atmospheric particles is considered to pose a health threat to humans and animals. In this context, it has been hypothesized that toxic chemicals such as polycyclic aromatic hydrocarbons (PAHs) play an important role. Some PAHs are known to be carcinogenic and it has been shown that carcinogenic effects of PAHs are mediated by the aryl hydrocarbon receptor (AhR). In this study, PM1 was collected at a rural and an urban traffic site during an intense winter smog period, in which concentration of PM1 often exceeded 50 μg m -3. We applied an in vitro reporter gene assay (DR-CALUX) to detect and quantify PM1-associated chemicals that induce AhR-mediated gene expression. This activity was expressed as CALUX equivalents of 2,3,7,8-tetrachlorodibenzodioxin (PM-TCDD-CEQs). In addition, concentrations of PAHs in the PM1 extracts were determined using gas chromatography/high-resolution mass spectrometry. Concentrations of PM-TCDD-CEQs ranged from 10 to 85 pg m -3 and from 19 to 87 pg m -3 at the urban and rural site, respectively. By the use of known relative potency factors, the measured concentration of a PAH was converted into a PAH-TCDD-CEQ concentration. ΣPAH-TCDD-CEQ and PM-TCDD-CEQ were highly correlated at both sites ( r2 = 0.90 and 0.69). The calculated ΣPAH-TCDD-CEQs explain between 2% and 20% of the measured PM-TCDD-CEQs. Benzo[ k]fluoranthene was the most important PAH causing approximately 60% of the total ΣPAH-TCDD-CEQ activity. In contrast to NO, CO, PM10, and PM1, the concentration of PM-TCDD-CEQs showed no significant difference between the two sites. No indications were found that road traffic emissions caused elevated concentrations of PM-TCDD-CEQs at the urban traffic site.

MICROBIAL METABOLISM OF AROMATIC COMPOUNDS I.

PubMed Central

Tabak, Henry H.; Chambers, Cecil W.; Kabler, Paul W.

1964-01-01

Tabak, Henry H. (Robert A. Taft Sanitary Engineering Center, Cincinnati, Ohio), Cecil W. Chambers, and Paul W. Kabler. Microbial metabolism of aromatic carbon compounds. I. Decomposition of phenolic compounds and aromatic hydrocarbons by phenol-adapted bacteria. J. Bacteriol. 87:910–919. 1964.—Bacteria from soil and related environments were selected or adapted to metabolize phenol, hydroxy phenols, nitrophenols, chlorophenols, methylphenols, alkylphenols, and arylphenols when cultured in mineral salts media with the specific substrate as the sole source of carbon. A phenol-adapted culture (substrate-induced enzyme synthesis proven) was challenged in respirometric tests with 104 related compounds; probable significant oxidative activity occurred with 65. Dihydric phenols were generally oxidized; trihydric phenols were not. Cresols and dimethylphenols were oxidized; adding a chloro group increased resistance. Benzoic and hydroxybenzoic acids were oxidized; sulfonated, methoxylated, nitro, and chlorobenzoic acids were not; m-toluic acid was utilized but not the o- and p-isomers. Benzaldehyde and p-hydroxybenzaldehyde were oxidized. In general, nitro- and chloro-substituted compounds and the benzenes were difficult to oxidize. PMID:14137630

Forty years of Clar's aromatic π-sextet rule

PubMed Central

Solà, Miquel

2013-01-01

In 1972 Erich Clar formulated his aromatic π-sextet rule that allows discussing qualitatively the aromatic character of benzenoid species. Now, 40 years later, Clar's aromatic π-sextet rule is still a source of inspiration for many chemists. This simple rule has been validated both experimentally and theoretically. In this review, we select some particular examples to highlight the achievement of Clar's aromatic π-sextet rule in many situations and we discuss two recent successful cases of its application. PMID:24790950

Bicyclic Baird-type aromaticity

NASA Astrophysics Data System (ADS)

Cha, Won-Young; Kim, Taeyeon; Ghosh, Arindam; Zhang, Zhan; Ke, Xian-Sheng; Ali, Rashid; Lynch, Vincent M.; Jung, Jieun; Kim, Woojae; Lee, Sangsu; Fukuzumi, Shunichi; Park, Jung Su; Sessler, Jonathan L.; Chandrashekar, Tavarekere K.; Kim, Dongho

2017-12-01

Classic formulations of aromaticity have long been associated with topologically planar conjugated macrocyclic systems. The theoretical possibility of so-called bicycloaromaticity was noted early on. However, it has yet to be demonstrated by experiment in a simple synthetic organic molecule. Conjugated organic systems are attractive for studying the effect of structure on electronic features. This is because, in principle, they can be modified readily through dedicated synthesis. As such, they can provide useful frameworks for testing by experiment with fundamental insights provided by theory. Here we detail the synthesis and characterization of two purely organic non-planar dithienothiophene-bridged [34]octaphyrins that permit access to two different aromatic forms as a function of the oxidation state. In their neutral forms, these congeneric systems contain competing 26 and 34 π-electronic circuits. When subject to two-electron oxidation, electronically mixed [4n+1]/[4n+1] triplet biradical species in the ground state are obtained that display global aromaticity in accord with Baird's rule.

Toward molecular mechanism of xenon anesthesia: a link to studies of xenon complexes with small aromatic molecules.

PubMed

Andrijchenko, Natalya N; Ermilov, Alexander Yu; Khriachtchev, Leonid; Räsänen, Markku; Nemukhin, Alexander V

2015-03-19

The present study illustrates the steps toward understanding molecular mechanism of xenon anesthesia by focusing on a link to the structures and spectra of intermolecular complexes of xenon with small aromatic molecules. A primary cause of xenon anesthesia is attributed to inhibition of N-methyl-D-aspartate (NMDA) receptors by an unknown mechanism. Following the results of quantum mechanics/molecular mechanics (QM/MM) and molecular dynamics (MD) calculations we report plausible xenon action sites in the ligand binding domain of the NMDA receptor, which are due to interaction of xenon atoms with aromatic amino-acid residues. We rely in these calculations on computational protocols adjusted in combined experimental and theoretical studies of intermolecular complexes of xenon with phenol. Successful reproduction of vibrational shifts in molecular species upon complexation with xenon measured in low-temperature matrices allowed us to select a proper functional form in density functional theory (DFT) approach for use in QM subsystems, as well as to calibrate force field parameters for MD simulations. The results of molecular modeling show that xenon atoms can compete with agonists for a place in the corresponding protein cavity, thus indicating their active role in anesthetic action.

Active and regulatory sites of cytosolic 5'-nucleotidase.

PubMed

Pesi, Rossana; Allegrini, Simone; Careddu, Maria Giovanna; Filoni, Daniela Nicole; Camici, Marcella; Tozzi, Maria Grazia

2010-12-01

Cytosolic 5'-nucleotidase (cN-II), which acts preferentially on 6-hydroxypurine nucleotides, is essential for the survival of several cell types. cN-II catalyses both the hydrolysis of nucleotides and transfer of their phosphate moiety to a nucleoside acceptor through formation of a covalent phospho-intermediate. Both activities are regulated by a number of phosphorylated compounds, such as diadenosine tetraphosphate (Ap₄A), ADP, ATP, 2,3-bisphosphoglycerate (BPG) and phosphate. On the basis of a partial crystal structure of cN-II, we mutated two residues located in the active site, Y55 and T56. We ascertained that the ability to catalyse the transfer of phosphate depends on the presence of a bulky residue in the active site very close to the aspartate residue that forms the covalent phospho-intermediate. The molecular model indicates two possible sites at which adenylic compounds may interact. We mutated three residues that mediate interaction in the first activation site (R144, N154, I152) and three in the second (F127, M436 and H428), and found that Ap₄A and ADP interact with the same site, but the sites for ATP and BPG remain uncertain. The structural model indicates that cN-II is a homotetrameric protein that results from interaction through a specific interface B of two identical dimers that have arisen from interaction of two identical subunits through interface A. Point mutations in the two interfaces and gel-filtration experiments indicated that the dimer is the smallest active oligomerization state. Finally, gel-filtration and light-scattering experiments demonstrated that the native enzyme exists as a tetramer, and no further oligomerization is required for enzyme activation. © 2010 The Authors Journal compilation © 2010 FEBS.

Water in the Active Site of Ketosteroid Isomerase

PubMed Central

Hanoian, Philip; Hammes-Schiffer, Sharon

2011-01-01

Classical molecular dynamics simulations were utilized to investigate the structural and dynamical properties of water in the active site of ketosteroid isomerase (KSI) to provide insight into the role of these water molecules in the enzyme-catalyzed reaction. This reaction is thought to proceed via a dienolate intermediate that is stabilized by hydrogen bonding with residues Tyr16 and Asp103. A comparative study was performed for the wild-type (WT) KSI and the Y16F, Y16S, and Y16F/Y32F/Y57F (FFF) mutants. These systems were studied with three different bound ligands: equilenin, which is an intermediate analog, and the intermediate states of two steroid substrates. Several distinct water occupation sites were identified in the active site of KSI for the WT and mutant systems. Three additional sites were identified in the Y16S mutant that were not occupied in WT KSI or the other mutants studied. The number of water molecules directly hydrogen bonded to the ligand oxygen was approximately two waters in the Y16S mutant, one water in the Y16F and FFF mutants, and intermittent hydrogen bonding of one water molecule in WT KSI. The molecular dynamics trajectories of the Y16F and FFF mutants reproduced the small conformational changes of residue 16 observed in the crystal structures of these two mutants. Quantum mechanical/molecular mechanical calculations of 1H NMR chemical shifts of the protons in the active site hydrogen-bonding network suggest that the presence of water in the active site does not prevent the formation of short hydrogen bonds with far-downfield chemical shifts. The molecular dynamics simulations indicate that the active site water molecules exchange much more frequently for WT KSI and the FFF mutant than for the Y16F and Y16S mutants. This difference is most likely due to the hydrogen-bonding interaction between Tyr57 and an active site water molecule that is persistent in the Y16F and Y16S mutants but absent in the FFF mutant and significantly less

Water in the active site of ketosteroid isomerase.

PubMed

Hanoian, Philip; Hammes-Schiffer, Sharon

2011-08-09

Classical molecular dynamics simulations were utilized to investigate the structural and dynamical properties of water in the active site of ketosteroid isomerase (KSI) to provide insight into the role of these water molecules in the enzyme-catalyzed reaction. This reaction is thought to proceed via a dienolate intermediate that is stabilized by hydrogen bonding with residues Tyr16 and Asp103. A comparative study was performed for the wild-type (WT) KSI and the Y16F, Y16S, and Y16F/Y32F/Y57F (FFF) mutants. These systems were studied with three different bound ligands: equilenin, which is an intermediate analog, and the intermediate states of two steroid substrates. Several distinct water occupation sites were identified in the active site of KSI for the WT and mutant systems. Three additional sites were identified in the Y16S mutant that were not occupied in WT KSI or the other mutants studied. The number of water molecules directly hydrogen bonded to the ligand oxygen was approximately two in the Y16S mutant and one in the Y16F and FFF mutants, with intermittent hydrogen bonding of one water molecule in WT KSI. The molecular dynamics trajectories of the Y16F and FFF mutants reproduced the small conformational changes of residue 16 observed in the crystal structures of these two mutants. Quantum mechanical/molecular mechanical calculations of (1)H NMR chemical shifts of the protons in the active site hydrogen-bonding network suggest that the presence of water in the active site does not prevent the formation of short hydrogen bonds with far-downfield chemical shifts. The molecular dynamics simulations indicate that the active site water molecules exchange much more frequently for WT KSI and the FFF mutant than for the Y16F and Y16S mutants. This difference is most likely due to the hydrogen-bonding interaction between Tyr57 and an active site water molecule that is persistent in the Y16F and Y16S mutants but absent in the FFF mutant and significantly less probable

Tuning a Protein-Labeling Reaction to Achieve Highly Site Selective Lysine Conjugation.

PubMed

Pham, Grace H; Ou, Weijia; Bursulaya, Badry; DiDonato, Michael; Herath, Ananda; Jin, Yunho; Hao, Xueshi; Loren, Jon; Spraggon, Glen; Brock, Ansgar; Uno, Tetsuo; Geierstanger, Bernhard H; Cellitti, Susan E

2018-04-16

Activated esters are widely used to label proteins at lysine side chains and N termini. These reagents are useful for labeling virtually any protein, but robust reactivity toward primary amines generally precludes site-selective modification. In a unique case, fluorophenyl esters are shown to preferentially label human kappa antibodies at a single lysine (Lys188) within the light-chain constant domain. Neighboring residues His189 and Asp151 contribute to the accelerated rate of labeling at Lys188 relative to the ≈40 other lysine sites. Enriched Lys188 labeling can be enhanced from 50-70 % to >95 % by any of these approaches: lowering reaction temperature, applying flow chemistry, or mutagenesis of specific residues in the surrounding protein environment. Our results demonstrated that activated esters with fluoro-substituted aromatic leaving groups, including a fluoronaphthyl ester, can be generally useful reagents for site-selective lysine labeling of antibodies and other immunoglobulin-type proteins. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Active Site Characterization of Proteases Sequences from Different Species of Aspergillus.

PubMed

Morya, V K; Yadav, Virendra K; Yadav, Sangeeta; Yadav, Dinesh

2016-09-01

A total of 129 proteases sequences comprising 43 serine proteases, 36 aspartic proteases, 24 cysteine protease, 21 metalloproteases, and 05 neutral proteases from different Aspergillus species were analyzed for the catalytically active site residues using MEROPS database and various bioinformatics tools. Different proteases have predominance of variable active site residues. In case of 24 cysteine proteases of Aspergilli, the predominant active site residues observed were Gln193, Cys199, His364, Asn384 while for 43 serine proteases, the active site residues namely Asp164, His193, Asn284, Ser349 and Asp325, His357, Asn454, Ser519 were frequently observed. The analysis of 21 metalloproteases of Aspergilli revealed Glu298 and Glu388, Tyr476 as predominant active site residues. In general, Aspergilli species-specific active site residues were observed for different types of protease sequences analyzed. The phylogenetic analysis of these 129 proteases sequences revealed 14 different clans representing different types of proteases with diverse active site residues.

On the stereochemical course of palladium-catalyzed cross-coupling of allylic silanolate salts with aromatic bromides.

PubMed

Denmark, Scott E; Werner, Nathan S

2010-03-17

The stereochemical course of palladium-catalyzed cross-coupling reactions of an enantioenriched, alpha-substituted, allylic silanolate salt with aromatic bromides has been investigated. The allylic silanolate salt was prepared in high geometrical (Z/E, 94:6) and high enantiomeric (94:6 er) purity by a copper-catalyzed S(N)2' reaction of a resolved allylic carbamate. Eight different aromatic bromides underwent cross-coupling with excellent constitutional site-selectivity and excellent stereospecificity. Stereochemical correlation established that the transmetalation event proceeds through a syn S(E)' mechanism which is interpreted in terms of an intramolecular delivery of the arylpalladium electrophile through a key intermediate that contains a discrete Si-O-Pd linkage.

Half-of-the-sites reactivity of outer-membrane phospholipase A against an active-site-directed inhibitor.

PubMed

Ubarretxena-Belandia, I; Cox, R C; Dijkman, R; Egmond, M R; Verheij, H M; Dekker, N

1999-03-01

The reaction of a novel active-site-directed phospholipase A1 inhibitor with the outer-membrane phospholipase A (OMPLA) was investigated. The inhibitor 1-p-nitrophenyl-octylphosphonate-2-tridecylcarbamoyl-3-et hanesulfonyl -amino-3-deoxy-sn-glycerol irreversibly inactivated OMPLA. The inhibition reaction did not require the cofactor calcium or an unprotonated active-site His142. The inhibition of the enzyme solubilized in hexadecylphosphocholine micelles was characterized by a rapid (t1/2 = 20 min) and complete loss of enzymatic activity, concurrent with the covalent modification of 50% of the active-site serines, as judged from the amount of p-nitrophenolate (PNP) released. Modification of the remaining 50% occurred at a much lower rate, indicative of half-of-the-sites reactivity against the inhibitor of this dimeric enzyme. Inhibition of monomeric OMPLA solubilized in hexadecyl-N,N-dimethyl-1-ammonio-3-propanesulfonate resulted in an equimolar monophasic release of PNP, concurrent with the loss of enzymatic activity (t1/2 = 14 min). The half-of-the-sites reactivity is discussed in view of the dimeric nature of this enzyme.

Physical activity and cancer risk: dose-response and cancer, all sites and site-specific.

PubMed

Thune, I; Furberg, A S

2001-06-01

The association between physical activity and overall and site-specific cancer risk is elaborated in relation to whether any observed dose-response association between physical activity and cancer can be interpreted in terms of how much physical activity (type, intensity, duration, frequency) is needed to influence site- and gender-specific cancer risk. Observational studies were reviewed that have examined the independent effect of the volume of occupational physical activity (OPA) and/or leisure time physical activity (LPA) on overall and site-specific cancer risk. The evidence of cohort and case-control studies suggests that both leisure time and occupational physical activity protect against overall cancer risk, with a graded dose-response association suggested in both sexes. Confounding effects such as diet, body weight, and parity are often included as a covariate in the analyses, with little influence on the observed associations. A crude graded inverse dose-response association was observed between physical activity and colon cancer in 48 studies including 40,674 colon/colorectal cancer cases for both sexes. A dose-response effect of physical activity on colon cancer risk was especially observed, when participation in activities of at least moderate activity (>4.5 MET) and demonstrated by activities expressed as MET-hours per week. An observed inverse association with a dose-response relationship between physical activity and breast cancer was also identified in the majority of the 41 studies including 108,031 breast cancer cases. The dose-response relationship was in particular observed in case-control studies and supported by observations in cohort studies when participation in activities of at least moderate activity (>4.5 MET) and demonstrated by activities expressed by MET-hours per week. This association between physical activity and breast cancer risk is possibly dependent on age at exposure, age at diagnosis, menopausal status and other effect

Phenylalanyl-Glycyl-Phenylalanine Tripeptide: A Model System for Aromatic-Aromatic Side Chain Interactions in Proteins

DOE Office of Scientific and Technical Information (OSTI.GOV)

Valdes, Haydee; Pluhackova, Kristyna; Hobza, Pavel

The performance of a wide range of quantum chemical calculations for the ab initio study of realistic model systems of aromatic-aromatic side chain interactions in proteins (in particular those π-π interactions occurring between adjacent residues along the protein sequence) is here assessed on the phenylalanyl-glycyl-phenylalanine (FGF) tripeptide. Energies and geometries obtained at different levels of theory are compared with CCSD(T)/CBS benchmark energies and RI-MP2/cc-pVTZ benchmark geometries, respectively. Consequently, a protocol of calculation alternative to the very expensive CCSD(T)/CBS is proposed. In addition to this, the preferred orientation of the Phe aromatic side chains is discussed and compared with previous resultsmore » on the topic.« less

Microbial activities and dissolved organic matter dynamics in oil-contaminated surface seawater from the Deepwater Horizon oil spill site.

PubMed

Ziervogel, Kai; McKay, Luke; Rhodes, Benjamin; Osburn, Christopher L; Dickson-Brown, Jennifer; Arnosti, Carol; Teske, Andreas

2012-01-01

The Deepwater Horizon oil spill triggered a complex cascade of microbial responses that reshaped the dynamics of heterotrophic carbon degradation and the turnover of dissolved organic carbon (DOC) in oil contaminated waters. Our results from 21-day laboratory incubations in rotating glass bottles (roller bottles) demonstrate that microbial dynamics and carbon flux in oil-contaminated surface water sampled near the spill site two weeks after the onset of the blowout were greatly affected by activities of microbes associated with macroscopic oil aggregates. Roller bottles with oil-amended water showed rapid formation of oil aggregates that were similar in size and appearance compared to oil aggregates observed in surface waters near the spill site. Oil aggregates that formed in roller bottles were densely colonized by heterotrophic bacteria, exhibiting high rates of enzymatic activity (lipase hydrolysis) indicative of oil degradation. Ambient waters surrounding aggregates also showed enhanced microbial activities not directly associated with primary oil-degradation (β-glucosidase; peptidase), as well as a twofold increase in DOC. Concurrent changes in fluorescence properties of colored dissolved organic matter (CDOM) suggest an increase in oil-derived, aromatic hydrocarbons in the DOC pool. Thus our data indicate that oil aggregates mediate, by two distinct mechanisms, the transfer of hydrocarbons to the deep sea: a microbially-derived flux of oil-derived DOC from sinking oil aggregates into the ambient water column, and rapid sedimentation of the oil aggregates themselves, serving as vehicles for oily particulate matter as well as oil aggregate-associated microbial communities.

Microbial Activities and Dissolved Organic Matter Dynamics in Oil-Contaminated Surface Seawater from the Deepwater Horizon Oil Spill Site

PubMed Central

Ziervogel, Kai; McKay, Luke; Rhodes, Benjamin; Osburn, Christopher L.; Dickson-Brown, Jennifer; Arnosti, Carol; Teske, Andreas

2012-01-01

The Deepwater Horizon oil spill triggered a complex cascade of microbial responses that reshaped the dynamics of heterotrophic carbon degradation and the turnover of dissolved organic carbon (DOC) in oil contaminated waters. Our results from 21-day laboratory incubations in rotating glass bottles (roller bottles) demonstrate that microbial dynamics and carbon flux in oil-contaminated surface water sampled near the spill site two weeks after the onset of the blowout were greatly affected by activities of microbes associated with macroscopic oil aggregates. Roller bottles with oil-amended water showed rapid formation of oil aggregates that were similar in size and appearance compared to oil aggregates observed in surface waters near the spill site. Oil aggregates that formed in roller bottles were densely colonized by heterotrophic bacteria, exhibiting high rates of enzymatic activity (lipase hydrolysis) indicative of oil degradation. Ambient waters surrounding aggregates also showed enhanced microbial activities not directly associated with primary oil-degradation (β-glucosidase; peptidase), as well as a twofold increase in DOC. Concurrent changes in fluorescence properties of colored dissolved organic matter (CDOM) suggest an increase in oil-derived, aromatic hydrocarbons in the DOC pool. Thus our data indicate that oil aggregates mediate, by two distinct mechanisms, the transfer of hydrocarbons to the deep sea: a microbially-derived flux of oil-derived DOC from sinking oil aggregates into the ambient water column, and rapid sedimentation of the oil aggregates themselves, serving as vehicles for oily particulate matter as well as oil aggregate-associated microbial communities. PMID:22509359

Active Site Metal Occupancy and Cyclic Di-GMP Phosphodiesterase Activity of Thermotoga maritima HD-GYP.

PubMed

Miner, Kyle D; Kurtz, Donald M

2016-02-16

HD-GYPs make up a subclass of the metal-dependent HD phosphohydrolase superfamily and catalyze conversion of cyclic di(3',5')-guanosine monophosphate (c-di-GMP) to 5'-phosphoguanylyl-(3'→5')-guanosine (pGpG) and GMP. Until now, the only reported crystal structure of an HD-GYP that also exhibits c-di-GMP phosphodiesterase activity contains a His/carboxylate ligated triiron active site. However, other structural and phylogenetic correlations indicate that some HD-GYPs contain dimetal active sites. Here we provide evidence that an HD-GYP c-di-GMP phosphodiesterase, TM0186, from Thermotoga maritima can accommodate both di- and trimetal active sites. We show that an as-isolated iron-containing TM0186 has an oxo/carboxylato-bridged diferric site, and that the reduced (diferrous) form is necessary and sufficient to catalyze conversion of c-di-GMP to pGpG, but that conversion of pGpG to GMP requires more than two metals per active site. Similar c-di-GMP phosphodiesterase activities were obtained with divalent iron or manganese. On the basis of activity correlations with several putative metal ligand residue variants and molecular dynamics simulations, we propose that TM0186 can accommodate both di- and trimetal active sites. Our results also suggest that a Glu residue conserved in a subset of HD-GYPs is required for formation of the trimetal site and can also serve as a labile ligand to the dimetal site. Given the anaerobic growth requirement of T. maritima, we suggest that this HD-GYP can function in vivo with either divalent iron or manganese occupying di- and trimetal sites.

Enzymic aromatization of 6-alkyl-substituted androgens, potent competitive and mechanism-based inhibitors of aromatase.

PubMed Central

Numazawa, M; Yoshimura, A; Oshibe, M

1998-01-01

To gain insight into the relationships between the aromatase inhibitory activity of 6-alkyl-substituted androgens, potent competitive inhibitors, and their ability to serve as a substrate of aromatase, we studied the aromatization of a series of 6alpha- and 6beta-alkyl (methyl, ethyl, n-propyl, n-pentyl and n-heptyl)-substituted androst-4-ene-3,17-diones (ADs) and their androsta-1,4-diene-3,17-dione (ADD) derivatives with human placental aromatase, by gas chromatography-mass spectrometry. Among the inhibitors examined, ADD and its 6alpha-alkyl derivatives with alkyl functions less than three carbons long, together with 6beta-methyl ADD, are suicide substrates of aromatase. All of the steroids, except for 6beta-n-pentyl ADD and its n-heptyl analogue as well as 6beta-n-heptyl AD, were found to be converted into the corresponding 6-alkyl oestrogens. The 6-methyl steroids were aromatized most efficiently in each series, and the aromatization rate essentially decreased in proportion to the length of the 6-alkyl chains in each series, where the 6alpha-alkyl androgens were more efficient substrates than the corresponding 6beta isomers. The Vmax of 6alpha-methyl ADD was approx. 2.5-fold that of the natural substrate AD and approx. 3-fold that of the parent ADD. On the basis of this, along with the facts that the rates of a mechanism-based inactivation of aromatase by ADD and its 6alpha-methyl derivative are similar, it is implied that alignment of 6alpha-methyl ADD in the active site could favour the pathway leading to oestrogen over the inactivation pathway, compared with that of ADD. The relative apparent Km values for the androgens obtained in this study are different from the relative Ki values obtained previously, indicating that there is a difference between the ability to serve as an inhibitor and the ability to serve as a substrate in the 6-alkyl androgen series. PMID:9405288

Volatile profiles of aromatic and non-aromatic rice

USDA-ARS?s Scientific Manuscript database

Rice is enjoyed by many people as a staple food because of its flavor and texture. Some scented varieties command a premium in the marketplace because of their distinctive aroma and flavor. The compound most commonly associated with the popcorn or nutty scent of aromatic rice is 2-acetyl-1-pyrroline...

Aliphatic, Cyclic, and Aromatic Organic Acids, Vitamins, and Carbohydrates in Soil: A Review

PubMed Central

Vranova, Valerie; Rejsek, Klement; Formanek, Pavel

2013-01-01

Organic acids, vitamins, and carbohydrates represent important organic compounds in soil. Aliphatic, cyclic, and aromatic organic acids play important roles in rhizosphere ecology, pedogenesis, food-web interactions, and decontamination of sites polluted by heavy metals and organic pollutants. Carbohydrates in soils can be used to estimate changes of soil organic matter due to management practices, whereas vitamins may play an important role in soil biological and biochemical processes. The aim of this work is to review current knowledge on aliphatic, cyclic, and aromatic organic acids, vitamins, and carbohydrates in soil and to identify directions for future research. Assessments of organic acids (aliphatic, cyclic, and aromatic) and carbohydrates, including their behaviour, have been reported in many works. However, knowledge on the occurrence and behaviour of D-enantiomers of organic acids, which may be abundant in soil, is currently lacking. Also, identification of the impact and mechanisms of environmental factors, such as soil water content, on carbohydrate status within soil organic matter remains to be determined. Finally, the occurrence of vitamins in soil and their role in biological and biochemical soil processes represent an important direction for future research. PMID:24319374

Aliphatic, cyclic, and aromatic organic acids, vitamins, and carbohydrates in soil: a review.

PubMed

Vranova, Valerie; Rejsek, Klement; Formanek, Pavel

2013-11-10

Organic acids, vitamins, and carbohydrates represent important organic compounds in soil. Aliphatic, cyclic, and aromatic organic acids play important roles in rhizosphere ecology, pedogenesis, food-web interactions, and decontamination of sites polluted by heavy metals and organic pollutants. Carbohydrates in soils can be used to estimate changes of soil organic matter due to management practices, whereas vitamins may play an important role in soil biological and biochemical processes. The aim of this work is to review current knowledge on aliphatic, cyclic, and aromatic organic acids, vitamins, and carbohydrates in soil and to identify directions for future research. Assessments of organic acids (aliphatic, cyclic, and aromatic) and carbohydrates, including their behaviour, have been reported in many works. However, knowledge on the occurrence and behaviour of D-enantiomers of organic acids, which may be abundant in soil, is currently lacking. Also, identification of the impact and mechanisms of environmental factors, such as soil water content, on carbohydrate status within soil organic matter remains to be determined. Finally, the occurrence of vitamins in soil and their role in biological and biochemical soil processes represent an important direction for future research.

Diffusional correlations among multiple active sites in a single enzyme.

PubMed

Echeverria, Carlos; Kapral, Raymond

2014-04-07

Simulations of the enzymatic dynamics of a model enzyme containing multiple substrate binding sites indicate the existence of diffusional correlations in the chemical reactivity of the active sites. A coarse-grain, particle-based, mesoscopic description of the system, comprising the enzyme, the substrate, the product and solvent, is constructed to study these effects. The reactive and non-reactive dynamics is followed using a hybrid scheme that combines molecular dynamics for the enzyme, substrate and product molecules with multiparticle collision dynamics for the solvent. It is found that the reactivity of an individual active site in the multiple-active-site enzyme is reduced substantially, and this effect is analyzed and attributed to diffusive competition for the substrate among the different active sites in the enzyme.

Role of Urea-Aromatic Stacking Interactions in Stabilizing the Aromatic Residues of the Protein in Urea-Induced Denatured State.

PubMed

Goyal, Siddharth; Chattopadhyay, Aditya; Kasavajhala, Koushik; Priyakumar, U Deva

2017-10-25

A delicate balance of different types of intramolecular interactions makes the folded states of proteins marginally more stable than the unfolded states. Experiments use thermal, chemical, or mechanical stress to perturb the folding equilibrium for examining protein stability and the protein folding process. Elucidation of the mechanism by which chemical denaturants unfold proteins is crucial; this study explores the nature of urea-aromatic interactions relevant in urea-assisted protein denaturation. Free energy profiles corresponding to the unfolding of Trp-cage miniprotein in the presence and absence of urea at three different temperatures demonstrate the distortion of the hydrophobic core to be a crucial step. Exposure of the Trp6 residue to the solvent is found to be favored in the presence of urea. Previous experiments showed that urea has a high affinity for aromatic groups of proteins. We show here that this is due to the remarkable ability of urea to form stacking and NH-π interactions with aromatic groups of proteins. Urea-nucleobase stacking interactions have been shown to be crucial in urea-assisted RNA unfolding. Examination of these interactions using microsecond-long unrestrained simulations shows that urea-aromatic stacking interactions are stabilizing and long lasting. Further MD simulations, thermodynamic integration, and quantum mechanical calculations on aromatic model systems reveal that such interactions are possible for all the aromatic amino acid side-chains. Finally, we validate the ubiquitous nature of urea-aromatic stacking interactions by analyzing experimental structures of urea transporters and proteins crystallized in the presence of urea or urea derivatives.

Conservative Tryptophan Mutants of the Protein Tyrosine Phosphatase YopH Exhibit Impaired WPD-Loop Function and Crystallize with Divanadate Esters in Their Active Sites

PubMed Central

Moise, Gwendolyn; Gallup, Nathan M.; Alexandrova, Anastassia N.; Hengge, Alvan C.; Johnson, Sean J.

2016-01-01

Catalysis in protein tyrosine phosphatases (PTPs) involves movement of a protein loop called the WPD loop that brings a conserved aspartic acid into the active site to function as a general acid. Mutation of the tryptophan in the WPD loop of the PTP YopH to any other residue with a planar, aromatic side chain (phenylalanine, tyrosine, or histidine) disables general acid catalysis. Crystal structures reveal these conservative mutations leave this critical loop in a catalytically unproductive, quasi-open position. Although the loop positions in crystal structures are similar for all three conservative mutants, the reasons inhibiting normal loop closure differ for each mutant. In the W354F and W354Y mutants, steric clashes result from six-membered rings occupying the position of the five-membered ring of the native indole side chain. The histidine mutant dysfunction results from new hydrogen bonds stabilizing the unproductive position. The results demonstrate how even modest modifications can disrupt catalytically important protein dynamics. Crystallization of all the catalytically compromised mutants in the presence of vanadate gave rise to vanadate dimers at the active site. In W354Y and W354H, a divanadate ester with glycerol is observed. Such species have precedence in solution and are known from the small molecule crystal database. Such species have not been observed in the active site of a phosphatase, as a functional phosphatase would rapidly catalyze their decomposition. The compromised functionality of the mutants allows the trapping of species that undoubtedly form in solution and are capable of binding at the active sites of PTPs, and, presumably, other phosphatases. In addition to monomeric vanadate, such higher-order vanadium-based molecules are likely involved in the interaction of vanadate with PTPs in solution. PMID:26445170

Scenario-based modelling of mass transfer mechanisms at a petroleum contaminated field site-numerical implications.

PubMed

Vasudevan, M; Nambi, Indumathi M; Suresh Kumar, G

2016-06-15

Knowledge about distribution of dissolved plumes and their influencing factors is essential for risk assessment and remediation of light non-aqueous phase liquid contamination in groundwater. Present study deals with the applicability of numerical model for simulating various hydro-geological scenarios considering non-uniform source distribution at a petroleum contaminated site in Chennai, India. The complexity associated with the hydrogeology of the site has limited scope for on-site quantification of petroleum pipeline spillage. The change in fuel composition under mass-transfer limited conditions was predicted by simultaneously comparing deviations in aqueous concentrations and activity coefficients (between Raoult's law and analytical approaches). The effects of source migration and weathering on the dissolution of major soluble fractions of petroleum fuel were also studied in relation to the apparent change in their activity coefficients and molar fractions. The model results were compared with field observations and found that field conditions were favourable for biodegradation, especially for the aromatic fraction (benzene and toluene (nearly 95% removal), polycyclic aromatic hydrocarbons (up to 65% removal) and xylene (nearly 45% removal). The results help to differentiate the effect of compositional non-ideality from rate-limited dissolution towards tailing of less soluble compounds (alkanes and trimethylbenzene). Although the effect of non-ideality decreased with distance from the source, the assumption of spatially varying residual saturation could effectively illustrate post-spill scenario by estimating the consequent decrease in mass transfer rate. Copyright © 2016 Elsevier Ltd. All rights reserved.

Influence of the physicochemical and aromatic properties on the chemical reactivity and its relation with carcinogenic and anticoagulant effect of 17β-aminoestrogens

NASA Astrophysics Data System (ADS)

Soriano-Correa, Catalina; Raya, Angélica; Barrientos-Salcedo, Carolina; Esquivel, Rodolfo O.

2014-06-01

Activity of steroid hormones is dependent upon a number of factors, as solubility, transport and metabolism. The functional differences caused by structural modifications could exert an influence on the chemical reactivity and biological effect. The goal of this work is to study the influence of the physicochemical and aromatic properties on the chemical reactivity and its relation with the carcinogenic risk that can associate with the anticoagulant effect of 17β-aminoestrogens using quantum-chemical descriptors at the DFT-B3LYP, BH&HLYP and M06-2X levels. The relative acidity of (H1) of the hydroxyl group increases with electron-withdrawing groups. Electron-donor groups favor the basicity. The steric hindrance of the substituents decreases the aromatic character and consequently diminution the carcinogenic effect. Density descriptors: hardness, electrophilic index, atomic charges, molecular orbitals, electrostatic potential and their geometric parameters permit analyses of the chemical reactivity and physicochemical features and to identify some reactive sites of 17β-aminoestrogens.

Extending (Q)SARs to incorporate proprietary knowledge for regulatory purposes: A case study using aromatic amine mutagenicity.

PubMed

Ahlberg, Ernst; Amberg, Alexander; Beilke, Lisa D; Bower, David; Cross, Kevin P; Custer, Laura; Ford, Kevin A; Van Gompel, Jacky; Harvey, James; Honma, Masamitsu; Jolly, Robert; Joossens, Elisabeth; Kemper, Raymond A; Kenyon, Michelle; Kruhlak, Naomi; Kuhnke, Lara; Leavitt, Penny; Naven, Russell; Neilan, Claire; Quigley, Donald P; Shuey, Dana; Spirkl, Hans-Peter; Stavitskaya, Lidiya; Teasdale, Andrew; White, Angela; Wichard, Joerg; Zwickl, Craig; Myatt, Glenn J

2016-06-01

Statistical-based and expert rule-based models built using public domain mutagenicity knowledge and data are routinely used for computational (Q)SAR assessments of pharmaceutical impurities in line with the approach recommended in the ICH M7 guideline. Knowledge from proprietary corporate mutagenicity databases could be used to increase the predictive performance for selected chemical classes as well as expand the applicability domain of these (Q)SAR models. This paper outlines a mechanism for sharing knowledge without the release of proprietary data. Primary aromatic amine mutagenicity was selected as a case study because this chemical class is often encountered in pharmaceutical impurity analysis and mutagenicity of aromatic amines is currently difficult to predict. As part of this analysis, a series of aromatic amine substructures were defined and the number of mutagenic and non-mutagenic examples for each chemical substructure calculated across a series of public and proprietary mutagenicity databases. This information was pooled across all sources to identify structural classes that activate or deactivate aromatic amine mutagenicity. This structure activity knowledge, in combination with newly released primary aromatic amine data, was incorporated into Leadscope's expert rule-based and statistical-based (Q)SAR models where increased predictive performance was demonstrated. Copyright © 2016 Elsevier Inc. All rights reserved.

Influence of polychlorinated aromatic compounds on the biotransformation and toxicity of organophosphorus pesticides (OP) to the Daphnia magna

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tonkopii, V.; Zagrebin, A.; Sherstneva, L.

1995-12-31

The effect of different polychlorinated aromatics (DDT, Aroclor 1254, certain polychlorinated biphenyls and dibenzofurans) on the toxicity of OP (DDVP paraoxon, malaoxon) to Daphnia magna was studied. Pretreatment of daphnids with chlorinated compounds during 72 hours in nontoxic concentrations (1/5--1/20 CL{sub 50}) has been shown to reduce the toxicity of OP for hydrobionts. For study of influence of chlorinated compounds on biotransformation of OP the activity of enzymes which are hydrolyzing the OP was investigated in Daphnia`s homogenates or microsomes. The activity of carboxylesterase (tributyrinase, aliesterase) and arylesterase (phosphorylphosphatase) with usage as substrates accordingly {alpha}-naphthylacetate and paraoxon was measured. Besidesmore » that the activity of cholinesterase with application of propionylthiocholine as substrate was determined. After polychlorinated aromatic compounds treatment of daphnids activities of both aryl-and carboxylesterase increased markedly. It decreased the inhibition of Daphnia`s cholinesterase caused by incubation with OP in concentrations 0.5--1.0 CL{sub 50}. Thus the induction by chlorinate aromatics of OP metabolizing enzymes seems to play the important role in reduction of OP toxicity to Daphnia magna. Perhaps the aryl- and carboxylesterase of Daphnia can be used as biomarkers of pollution by polychlorinated aromatics in water.« less

IMPACTS OF AGING ON IN VIVO AND IN VITRO MEASUREMENTS OF SOIL-BOUND POLYCYCLIC AROMATIC HYDROCARBON AVAILABILITY

EPA Science Inventory

Ingestion of contaminated soil is an exposure pathway at approximately one-half of the Superfund sites in the United States. This study was designed to evaluate the impacts of aging in soil on the availability of polycyclic aromatic hydrocarbons (PAHs). Two coal tar (CT)-amended ...

Influence of substrate modification and C-terminal truncation on the active site structure of substrate-bound heme oxygenase from Neisseriae meningitidis; A 1H NMR study†

PubMed Central

Peng, Dungeng; Satterlee, James D.; Ma, Li-Hua; Dallas, Jerry L.; Smith, Kevin M.; Zhang, Xuhong; Sato, Michihiko; La Mar, Gerd N.

2011-01-01

Heme oxygenase, HO, from the pathogenic bacterium N. meningitidis, NmHO, which secures host iron, shares many properties with mammalian HOs, but also exhibits some key differences. The crystal structure appears more compact and the crystal-undetected C-terminus interacts with substrate in solution. The unique nature of substrate-protein, specifically pyrrole-I/II-helix-2, peripheral interactions in NmHO are probed by 2D 1H NMR to reveal unique structural features controlling substrate orientation. The thermodynamics of substrate orientational isomerism are mapped for substrates with individual vinyl → methyl → hydrogen substitutions and with enzyme C-terminal deletions. NmHO exhibits significantly stronger orientational preference, reflecting much stronger and selective pyrrole-I/II interactions with the protein matrix, than in mammalian HOs. Thus, replacing bulky vinyls with hydrogens results in a 180° rotation of substrate about the α,γ-meso axis in the active site. A "collapse" of the substrate pocket as substrate size decreases is reflected in movement of helix-2 toward the substrate as indicated by significant and selective increased NOESY cross peak intensity, increase in steric Fe-CN tilt reflected in the orientation of the major magnetic axis, and decrease in steric constraints controlling the rate of aromatic ring reorientation. The active site of NmHO appears "stressed" for native protohemin and its "collapse" upon replacing vinyls by hydrogen leads to a factor ~102 increase in substrate affinity. Interaction of the C-terminus with the active site destabilizes the crystallographic protohemin orientation by ~0.7 kcal/mol, which is consistent with optimizing the His207-Asp27 H-bond. Implications of the active site "stress" for product release are discussed. PMID:21870860

Direct instrumental identification of catalytically active surface sites

NASA Astrophysics Data System (ADS)

Pfisterer, Jonas H. K.; Liang, Yunchang; Schneider, Oliver; Bandarenka, Aliaksandr S.

2017-09-01

The activity of heterogeneous catalysts—which are involved in some 80 per cent of processes in the chemical and energy industries—is determined by the electronic structure of specific surface sites that offer optimal binding of reaction intermediates. Directly identifying and monitoring these sites during a reaction should therefore provide insight that might aid the targeted development of heterogeneous catalysts and electrocatalysts (those that participate in electrochemical reactions) for practical applications. The invention of the scanning tunnelling microscope (STM) and the electrochemical STM promised to deliver such imaging capabilities, and both have indeed contributed greatly to our atomistic understanding of heterogeneous catalysis. But although the STM has been used to probe and initiate surface reactions, and has even enabled local measurements of reactivity in some systems, it is not generally thought to be suited to the direct identification of catalytically active surface sites under reaction conditions. Here we demonstrate, however, that common STMs can readily map the catalytic activity of surfaces with high spatial resolution: we show that by monitoring relative changes in the tunnelling current noise, active sites can be distinguished in an almost quantitative fashion according to their ability to catalyse the hydrogen-evolution reaction or the oxygen-reduction reaction. These data allow us to evaluate directly the importance and relative contribution to overall catalyst activity of different defects and sites at the boundaries between two materials. With its ability to deliver such information and its ready applicability to different systems, we anticipate that our method will aid the rational design of heterogeneous catalysts.

The identity of the active site of oxalate decarboxylase and the importance of the stability of active-site lid conformations1

PubMed Central

Just, Victoria J.; Burrell, Matthew R.; Bowater, Laura; McRobbie, Iain; Stevenson, Clare E. M.; Lawson, David M.; Bornemann, Stephen

2007-01-01

Oxalate decarboxylase (EC 4.1.1.2) catalyses the conversion of oxalate into carbon dioxide and formate. It requires manganese and, uniquely, dioxygen for catalysis. It forms a homohexamer and each subunit contains two similar, but distinct, manganese sites termed sites 1 and 2. There is kinetic evidence that only site 1 is catalytically active and that site 2 is purely structural. However, the kinetics of enzymes with mutations in site 2 are often ambiguous and all mutant kinetics have been interpreted without structural information. Nine new site-directed mutants have been generated and four mutant crystal structures have now been solved. Most mutants targeted (i) the flexibility (T165P), (ii) favoured conformation (S161A, S164A, D297A or H299A) or (iii) presence (Δ162–163 or Δ162–164) of a lid associated with site 1. The kinetics of these mutants were consistent with only site 1 being catalytically active. This was particularly striking with D297A and H299A because they disrupted hydrogen bonds between the lid and a neighbouring subunit only when in the open conformation and were distant from site 2. These observations also provided the first evidence that the flexibility and stability of lid conformations are important in catalysis. The deletion of the lid to mimic the plant oxalate oxidase led to a loss of decarboxylase activity, but only a slight elevation in the oxalate oxidase side reaction, implying other changes are required to afford a reaction specificity switch. The four mutant crystal structures (R92A, E162A, Δ162–163 and S161A) strongly support the hypothesis that site 2 is purely structural. PMID:17680775

Role of active site rigidity in activity: MD simulation and fluorescence study on a lipase mutant.

PubMed

Kamal, Md Zahid; Mohammad, Tabrez Anwar Shamim; Krishnamoorthy, G; Rao, Nalam Madhusudhana

2012-01-01

Relationship between stability and activity of enzymes is maintained by underlying conformational flexibility. In thermophilic enzymes, a decrease in flexibility causes low enzyme activity while in less stable proteins such as mesophiles and psychrophiles, an increase in flexibility is associated with enhanced enzyme activity. Recently, we identified a mutant of a lipase whose stability and activity were enhanced simultaneously. In this work, we probed the conformational dynamics of the mutant and the wild type lipase, particularly flexibility of their active site using molecular dynamic simulations and time-resolved fluorescence techniques. In contrast to the earlier observations, our data show that active site of the mutant is more rigid than wild type enzyme. Further investigation suggests that this lipase needs minimal reorganization/flexibility of active site residues during its catalytic cycle. Molecular dynamic simulations suggest that catalytically competent active site geometry of the mutant is relatively more preserved than wild type lipase, which might have led to its higher enzyme activity. Our study implies that widely accepted positive correlation between conformation flexibility and enzyme activity need not be stringent and draws attention to the possibility that high enzyme activity can still be accomplished in a rigid active site and stable protein structures. This finding has a significant implication towards better understanding of involvement of dynamic motions in enzyme catalysis and enzyme engineering through mutations in active site.

Identification of cancer chemopreventive isothiocyanates as direct inhibitors of the arylamine N-acetyltransferase-dependent acetylation and bioactivation of aromatic amine carcinogens.

PubMed

Duval, Romain; Xu, Ximing; Bui, Linh-Chi; Mathieu, Cécile; Petit, Emile; Cariou, Kevin; Dodd, Robert H; Dupret, Jean-Marie; Rodrigues-Lima, Fernando

2016-02-23

Aromatic amines (AAs) are chemicals of industrial, pharmacological and environmental relevance. Certain AAs, such as 4-aminobiphenyl (4-ABP), are human carcinogens that require enzymatic metabolic activation to reactive chemicals to form genotoxic DNA adducts. Arylamine N-acetyltransferases (NAT) are xenobiotic metabolizing enzymes (XME) that play a major role in this carcinogenic bioactivation process. Isothiocyanates (ITCs), including benzyl-ITC (BITC) and phenethyl-ITC (PEITC), are phytochemicals known to have chemopreventive activity against several aromatic carcinogens. In particular, ITCs have been shown to modify the bioactivation and subsequent mutagenicity of carcinogenic AA chemicals such as 4-ABP. However, the molecular and biochemical mechanisms by which these phytochemicals may modulate AA carcinogens bioactivation and AA-DNA damage remains poorly understood. This manuscript provides evidence indicating that ITCs can decrease the metabolic activation of carcinogenic AAs via the irreversible inhibition of NAT enzymes and subsequent alteration of the acetylation of AAs. We demonstrate that BITC and PEITC react with NAT1 and inhibit readily its acetyltransferase activity (k(i) = 200 M(-1).s(-1) and 66 M(-1).s(-1) for BITC and PEITC, respectively). Chemical labeling, docking approaches and substrate protection assays indicated that inhibition of the acetylation of AAs by NAT1 was due to the chemical modification of the enzyme active site cysteine. Moreover, analyses of AAs acetylation and DNA adducts in cells showed that BITC was able to modulate the endogenous acetylation and bioactivation of 4-ABP. In conclusion, we show that direct inhibition of NAT enzymes may be an important mechanism by which ITCs exert their chemopreventive activity towards AA chemicals.

Bioremediation in oil-contaminated sites: bacteria and surfactant accelerated remediation

NASA Astrophysics Data System (ADS)

Strong-Gunderson, Janet M.; Guzman, Francisco

1996-11-01

In Mexico, there are several environmental issues which are being addressed under the current governmental legislation. One important issue is restoring sites belonging to Petroleos Mexicanos (PEMEX). PEMEX is a large government owned oil company that regulates and manages the oil reserves. These sites are primarily contaminated with weathered hydrocarbons which are a consequence of extracting millions of barrels of oil. Within the southern regions of Mexico there are sites which were contaminated by activities and spills that have occurred during the past 30 years. PEMEX has taken the leadership in correcting environmental problems and is very concerned about cleaning up the contaminated sites as quickly as possible. The most significant contaminated sites are located to the north of Veracruz and south of Tabasco. These sites areas are close to refineries or locations of oil exploration. The primary category of contaminants are hydrocarbons, among them asphaltens, aromatic and other contaminants. The concentration of the contaminants varies depending on the location of the sites, but it can reach as high as 500,000 ppm. PEMEX has been searching for appropriate, and cost- effective technologies to clean up these sites. Biologically based remediation activities are of primary interest to PEMEX. However, other treatment technologies such as chemical-physical methods, encapsulation and incineration are also being considered. The present report summarizes preliminary experiments that measured the feasibility of bioremediation for a contaminated site in southern Mexico.

Separation of aromatic carboxylic acids using quaternary ammonium salts on reversed-phase HPLC. 1. Separation behavior of aromatic carboxylic acids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kawamura, K.; Okuwaki, A.; Verheyen, T.

In order to develop separation processes and analytical methods for aromatic carboxylic acids for the coal oxidation products, the separation behavior of aromatic carboxylic acids on a reversed-phase HPLC using eluent containing quaternary ammonium salt has been investigated. The retention mechanism of aromatic carboxylic acids was discussed on the basis of both ion-pair partition model and ion-exchange model. The retention behavior of aromatic carboxylic acids possessing one (or two) carboxylic acid group(s) followed the ion-pair partition model, where linear free energy relationship was observed between the capacity factor and the extraction equilibrium constants of benzoic acid and naphthalene carboxylic acid.more » Besides, the retention behavior followed ion-exchange model with increasing the number of carboxylic acids, where the capacity factor of benzene polycarboxylic acids is proportional to the association constants between aromatic acids and quaternary ammonium ions calculated on the basis of an electrostatic interaction model.« less

ortho- and meta-substituted aromatic thiols are efficient redox buffers that increase the folding rate of a disulfide-containing protein.

PubMed

Gough, Jonathan D; Barrett, Elvis J; Silva, Yenia; Lees, Watson J

2006-08-20

Thiol based redox buffers are used to enhance the folding rates of disulfide-containing proteins in vitro. Traditionally, small molecule aliphatic thiols such as glutathione are employed. Recently, we have demonstrated that aromatic thiols can further enhance protein-folding rates. In the presence of para-substituted aromatic thiols the folding rate of a disulfide-containing protein was increased by 4-23 times over that measured for glutathione. However, several important practical issues remain to be addressed. Aromatic thiols have never been tested in the presence of denaturants such as guanidine hydrochloride. Only two of the para-substituted aromatic thiols previously examined are commercially available. To expand the number of aromatic thiols for protein folding, several commercially available meta- and ortho-substituted aromatic thiols were studied. Furthermore, an ortho-substituted aromatic thiol, easily obtained from inexpensive starting materials, was investigated. Folding rates of scrambled ribonuclease A at pH 6.0, 7.0 and 7.7, with ortho- and meta-substituted aromatic thiols, were up to 10 times greater than those with glutathione. In the presence of the common denaturant guanidine hydrochloride (0.5M) aromatic thiols provided 100% yield of active protein while maintaining equivalent folding rates.

Consensus sediment quality guidelines for polycyclic aromatic hydrocarbon mixtures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Swartz, R.C.

1999-04-01

Sediment quality guidelines (SQGs) for polycyclic aromatic hydrocarbons (PAHs) have been derived from a variety of laboratory, field, and theoretical foundations. They include the screening level concentration, effects ranges-low and -median, equilibrium partitioning concentrations, apparent effects threshold, {Sigma}PAH model, and threshold and probable effects levels. The resolution of controversial differences among the PAH SQGs lies in an understanding of the effects of mixtures. Polycyclic aromatic hydrocarbons virtually always occur in field-collected sediment as a complex mixture of covarying compounds. When expressed as a mixture concentration, that is, total PAH (TPAH), the guidelines form three clusters that were intended in theirmore » original derivations to represent threshold (TEC = 290 {micro}g/g organic carbon [OC]), median (MEC = 1,800 {micro}g/g OC), and extreme (EEC = 10,000 {micro}g/g OC) effects concentrations. The TEC/MEC/EEC consensus guidelines provide a unifying synthesis of other SQGs, reflect causal rather than correlative effects, account for mixtures, and predict sediment toxicity and benthic community perturbations at sites of PAH contamination. The TEC offers the most useful SQG because PAH mixtures are unlikely to cause adverse effects on benthic ecosystems below the TEC.« less

Chemoenzymatic syntheses of prenylated aromatic small molecules using Streptomyces prenyltransferases with relaxed substrate specificities

PubMed Central

Kumano, Takuto; Richard, Stéphane B.; Noel, Joseph P.; Nishiyama, Makoto; Kuzuyama, Tomohisa

2010-01-01

NphB is a soluble prenyltransferase from Streptomyces sp. strain CL190 that attaches a geranyl group to a 1,3,6,8-tetrahydroxynaphthalene-derived polyketide during the biosynthesis of anti-oxidant naphterpin. Here we report multiple chemoenzymatic syntheses of various prenylated compounds from aromatic substrates including flavonoids using two prenyltransferases NphB and SCO7190, a NphB homolog from Streptomyces coelicolor A3(2), as biocatalysts. NphB catalyzes carbon–carbon-based and carbon–oxygen-based geranylation of a diverse collection of hydroxyl-containing aromatic acceptors. Thus, this simple method using the prenyltransferases can be used to explore novel prenylated aromatic compounds with biological activities. Kinetic studies with NphB reveal that the prenylation reaction follows a sequential ordered mechanism. PMID:18682327

Analogies between Vanadoborates and Planar Aromatic Hydrocarbons: A High-Spin Analogue of Aromaticity.

PubMed

King, R Bruce

2017-12-23

The vanadium-vanadium interactions in the polygonal aggregates of d¹ vanadium(IV) atoms, with a total of 4 k + 2 vanadium electrons ( k an integer) imbedded in an electronically inactive borate matrix in certain vanadoborate structures are analogous to the ring carbon-carbon interactions in diamagnetic planar cyclic hydrocarbons. They thus represent a high-spin analogue of aromaticity. Thus, the vanadoborate anion [V₆B 20 O 50 H₈] 8- with six V(IV) electrons (i.e., 4 k + 2 for k = 1) contains a macrohexagon of d¹ V(IV) atoms with four unpaired electrons. This high-spin system is related to the low-spin aromaticity in the diamagnetic benzene having six π electrons. Similarly, the vanadoborate anion [V 10 B 28 O 74 H₈] 16- with ten V(IV) electrons (i.e., 4 k + 2 for k = 2) contains a macrodecagon of d¹ V(IV) atoms with eight unpaired electrons. Again, this high-spin system is related to the aromaticity in the diamagnetic 1,6-methanol[10]annulene, having ten π electrons.

Diversity of organotrophic bacteria, activity of dehydrogenases and urease as well as seed germination and root growth Lepidium sativum, Sorghum saccharatum and Sinapis alba under the influence of polycyclic aromatic hydrocarbons.

PubMed

Lipińska, Aneta; Wyszkowska, Jadwiga; Kucharski, Jan

2015-12-01

Polycyclic aromatic hydrocarbons are organic compounds with highly toxic, carcinogenic, and mutagenic properties, which adversely affect the basic biological parameters of the soil, including the count of microorganisms, and the enzymatic activity. In addition to disturbances to the biological activity of the soil, PAHs may also exhibit toxic effects on plants. In view of the above, the study involved testing aimed at the determination of the effects of polycyclic aromatic hydrocarbons in a form of naphthalene, phenanthrene, anthracene and pyrene on the count, colony development (CD) index, ecophysiological (EP) diversity index of organotrophic bacteria, and the activity of soil dehydrogenases and soil urease. Moreover, an attempt was made to determine the soil's resistance based on the activity of the above-listed enzymes, and the effect of polycyclic aromatic hydrocarbons on seed germination and root growth was assessed by Lepidium sativum, Sorghum saccharatum, and Sinapis alba. In addition, the species of bacteria found in a soil subjected to strong pressure of polycyclic aromatic hydrocarbons were isolated. The experiment was performed in a laboratory on samples of loamy sand. Polycyclic aromatic hydrocarbons were introduced into the soil in an amount of 0, 1000, 2000, and 4000 mg kg(-1) of soil dry matter. Germination and growth of cress (L. sativum), white mustard (S. alba), and sweet sorghum (S. saccharatum) were determined using Phytotoxkit tests. It was found that the tested PAHs increased the average colony counts of organotrophic soil bacteria; pyrene did so to the greatest extent (2.2-fold relative to non-contaminated soil), phenanthrene to the smallest extent (1.4-fold relative to non-contaminated soil). None of the PAHs changed the value of the bacterial colony development (CD) index, while anthracene and pyrene increased the value of the eco-physiological (EP) diversity indicator. PAHs lowered the activity of the tested enzymes. The activity of

40 CFR 61.154 - Standard for active waste disposal sites.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 8 2011-07-01 2011-07-01 false Standard for active waste disposal... for Asbestos § 61.154 Standard for active waste disposal sites. Each owner or operator of an active... visible emissions to the outside air from any active waste disposal site where asbestos-containing waste...

40 CFR 61.154 - Standard for active waste disposal sites.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 9 2013-07-01 2013-07-01 false Standard for active waste disposal... for Asbestos § 61.154 Standard for active waste disposal sites. Each owner or operator of an active... visible emissions to the outside air from any active waste disposal site where asbestos-containing waste...

40 CFR 61.154 - Standard for active waste disposal sites.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 9 2012-07-01 2012-07-01 false Standard for active waste disposal... for Asbestos § 61.154 Standard for active waste disposal sites. Each owner or operator of an active... visible emissions to the outside air from any active waste disposal site where asbestos-containing waste...

40 CFR 61.154 - Standard for active waste disposal sites.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 8 2010-07-01 2010-07-01 false Standard for active waste disposal... for Asbestos § 61.154 Standard for active waste disposal sites. Each owner or operator of an active... visible emissions to the outside air from any active waste disposal site where asbestos-containing waste...

40 CFR 61.154 - Standard for active waste disposal sites.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 9 2014-07-01 2014-07-01 false Standard for active waste disposal... for Asbestos § 61.154 Standard for active waste disposal sites. Each owner or operator of an active... visible emissions to the outside air from any active waste disposal site where asbestos-containing waste...

Activated carbon as catalyst for microwave-assisted wet peroxide oxidation of aromatic hydrocarbons.

PubMed

Garcia-Costa, Alicia L; Lopez-Perela, Lucia; Xu, Xiyan; Zazo, Juan A; Rodriguez, Juan J; Casas, Jose A

2018-05-21

This paper addresses the removal of four aromatic hydrocarbons typically found in petrochemical wastewater: benzene (B), toluene (T), o-xylene (X), and naphthalene (N), by microwave-assisted catalytic wet peroxide oxidation (MW-CWPO) using activated carbon (AC) as catalyst. Under the studied conditions, complete pollutant elimination (B, 1.28 mM; T, 1.09 mM; X, 0.94 mM; and N, 0.78 mM) was achieved, with more than 90% TOC removal after only 15-min reaction time, working at 120 °C, pH 0  = 3, AC at 1 g L -1 , and H 2 O 2 at the stoichiometric dose. Furthermore, in the case of toluene, naphthalene, and xylene, the hydroxylation and breakdown of the ring is very rapid and toxic intermediates were not detected. The process follows two steps: (i) pollutant adsorption onto AC followed by (ii) adsorbed compounds oxidation. Thus, MW-CWPO with AC as catalyst appears a promising way for a fast and effective process for B, T, X, and N removal in aqueous phase.

Environmental nitration processes enhance the mutagenic potency of aromatic compounds.

PubMed

Bonnefoy, Aurélie; Chiron, Serge; Botta, Alain

2012-05-01

This work is an attempt to establish if aromatic nitration processes are always associated with an increase of genotoxicity. We determined the mutagenic and genotoxic effects of Benzene (B), Nitrobenzene (NB), Phenol (P), 2-Nitrophenol (2-NP), 2,4-Dinitrophenol (2,4-DNP), Pyrene (Py), 1-Nitropyrene (1-NPy), 1,3-Dinitropyrene (1,3-DNPy), 1,6-Dinitropyrene (1,6-DNPy), and 1,8-Dinitropyrene (1,8-DNPy). The mutagenic activities were evaluated with umuC test in presence and in absence of metabolic activation with S9 mix. Then, we used both cytokinesis-blocked micronucleus (CBMN) assay, in combination with fluorescent in situ hybridization (FISH) of human pan-centromeric DNA probes on human lymphocytes in order to evaluate the genotoxic effects. Analysis of all results shows that nitro polycyclic aromatic hydrocarbons (PAHs) are definitely environmental genotoxic/mutagenic hazards and confirms that environmental aromatic nitration reactions lead to an increase in genotoxicity and mutagenicity properties. Particularly 1-NPy and 1,8-DNPy can be considered as human potential carcinogens. They seem to be significant markers of the genotoxicity, mutagenicity, and potential carcinogenicity of complex PAHs mixtures present in traffic emission and industrial environment. In prevention of environmental carcinogenic risk 1-NPy and 1,8-DNPy must therefore be systematically analyzed in environmental complex mixtures in association with combined umuC test, CBMN assay, and FISH on cultured human lymphocytes. © 2010 Wiley Periodicals, Inc. Environ Toxicol, 2012. Copyright © 2010 Wiley Periodicals, Inc.

Sequence-specific 1H-NMR assignments for the aromatic region of several biologically active, monomeric insulins including native human insulin.

PubMed

Roy, M; Lee, R W; Kaarsholm, N C; Thøgersen, H; Brange, J; Dunn, M F

1990-06-12

The aromatic region of the 1H-FT-NMR spectrum of the biologically fully-potent, monomeric human insulin mutant, B9 Ser----Asp, B27 Thr----Glu has been investigated in D2O. At 1 to 5 mM concentrations, this mutant insulin is monomeric above pH 7.5. Coupling and amino acid classification of all aromatic signals is established via a combination of homonuclear one- and two-dimensional methods, including COSY, multiple quantum filters, selective spin decoupling and pH titrations. By comparisons with other insulin mutants and with chemically modified native insulins, all resonances in the aromatic region are given sequence-specific assignments without any reliance on the various crystal structures reported for insulin. These comparisons also give the sequence-specific assignments of most of the aromatic resonances of the mutant insulins B16 Tyr----Glu, B27 Thr----Glu and B25 Phe----Asp and the chemically modified species des-(B23-B30) insulin and monoiodo-Tyr A14 insulin. Chemical dispersion of the assigned resonances, ring current perturbations and comparisons at high pH have made possible the assignment of the aromatic resonances of human insulin, and these studies indicate that the major structural features of the human insulin monomer (including those critical to biological function) are also present in the monomeric mutant.

Carcinogenic potential of hydrotreated petroleum aromatic extracts.

PubMed Central

Doak, S M; Hend, R W; van der Wiel, A; Hunt, P F

1985-01-01

Five experimental petroleum extracts were produced from luboil distillates derived from Middle East paraffinic crude by solvent extraction and severe hydrotreatment. The polycyclic aromatic content (PCA) of the extracts was determined by dimethyl sulphoxide extraction and ranged from 3.7-9.2% w/w. The five extracts were evaluated for their potential to induce cutaneous and systemic neoplasia in female mice derived from Carworth Farm No 1 strain (CF1). The test substances were applied undiluted (0.2 ml per application) to the shorn dorsal skin twice weekly for up to 78 weeks, with 48 mice in each treatment group and 96 in the untreated control group; two further groups, each of 48 mice, were similarly treated either with a non-hydrotreated commercial aromatic extract (PCA content, 19.7% w/v) or with a low dose of benzo(a)pyrene (12.5 micrograms/ml acetone). The mice were housed individually in polypropylene cages in specified pathogen free conditions. The incidence of cutaneous and systemic tumours was determined from histological analysis of haematoxylin and eosin stained tissue sections. The results were correlated with the PCA content of the extracts and compared with those from female mice exposed to a non-hydrotreated commercial aromatic extract. Four of the hydrotreated extracts were carcinogenic for murine skin; the two products with the lower PCA contents were less carcinogenic than the products with the higher PCA contents and all were less carcinogenic than the commercial extract. One extract with the lowest PCA content was non-carcinogenic. Thus refining by severe hydrotreatment was an effective method of reducing the carcinogenic potential of petroleum aromatic extracts. Although other physicochemical properties may influence the biological activity of oil products, the PCA content determined by dimethyl sulphoxide extraction may be a useful indicator of the potential of oil products to induce cutaneous tumours in experimental animals. There was no

Dendrimer encapsulated Silver nanoparticles as novel catalysts for reduction of aromatic nitro compounds

NASA Astrophysics Data System (ADS)

Asharani, I. V.; Thirumalai, D.; Sivakumar, A.

2017-11-01

Polyethylene glycol (PEG) core dendrimer encapsulated silver nanoparticles (AgNPs) were synthesized through normal chemical reduction method, where dendrimer acts as reducing and stabilizing agent. The encapsulated AgNPs were well characterized using TEM, DLS and XPS techniques. The synthesized AgNPs showed excellent catalytic activity towards the reduction of aromatic nitro compounds with sodium borohydride as reducing agent and the results substantiate that dendrimer encapsulated AgNPs can be an effective catalyst for the substituted nitro aromatic reduction reactions. Also the kinetics of different nitro compounds reductions was studied and presented.

PERFLUORINATED AROMATIC COMPOUNDS

DTIC Science & Technology

decafluorodiphenylamine, 3,3’,4,4’-tetra substituted- hexafluorobiphenyls, tetrafluororesorcinol, perfluoroaromatic thioethers, and dithiols. These...and other perfluorinated aromatic compounds are the intermediates employed in the synthesis of perfluorinated model compounds and polymers.

Oxidation of Naphthenoaromatic and Methyl-Substituted Aromatic Compounds by Naphthalene 1,2-Dioxygenase

PubMed Central

Selifonov, S. A.; Grifoll, M.; Eaton, R. W.; Chapman, P. J.

1996-01-01

Oxidation of acenaphthene, acenaphthylene, and fluorene was examined with recombinant strain Pseudomonas aeruginosa PAO1(pRE695) expressing naphthalene dioxygenase genes cloned from plasmid NAH7. Acenaphthene underwent monooxygenation to 1-acenaphthenol with subsequent conversion to 1-acenaphthenone and cis- and trans-acenaphthene-1,2-diols, while acenaphthylene was dioxygenated to give cis-acenaphthene-1,2-diol. Nonspecific dehydrogenase activities present in the host strain led to the conversion of both of the acenaphthene-1,2-diols to 1,2-acenaphthoquinone. The latter was oxidized spontaneously to naphthalene-1,8-dicarboxylic acid. No aromatic ring dioxygenation products were detected from acenaphthene and acenaphthylene. Mixed monooxygenase and dioxygenase actions of naphthalene dioxygenase on fluorene yielded products of benzylic 9-monooxygenation, aromatic ring dioxygenation, or both. The action of naphthalene dioxygenase on a variety of methyl-substituted aromatic compounds, including 1,2,4-trimethylbenzene and isomers of dimethylnaphthalene, resulted in the formation of benzylic alcohols, i.e., methyl group monooxygenation products, which were subsequently converted to the corresponding carboxylic acids by dehydrogenase(s) in the host strain. Benzylic monooxygenation of methyl groups was strongly predominant over aromatic ring dioxygenation and essentially nonspecific with respect to the substitution pattern of the aromatic substrates. In addition to monooxygenating benzylic methyl and methylene groups, naphthalene dioxygenase behaved as a sulfoxygenase, catalyzing monooxygenation of the sulfur heteroatom of 3-methylbenzothiophene. PMID:16535238

Aromatic polyimides containing a dimethylsilane-linked dianhydride

NASA Technical Reports Server (NTRS)

St.clair, Anne K. (Inventor); St.clair, Terry L. (Inventor); Pratt, J. Richard (Inventor)

1989-01-01

A high-temperature stable, optically transparent, low dielectric aromatic polyimide is prepared by chemically combining equimolar quantities of an aromatic dianhydride reactant and an aromatic diamine reactant, which are selected so that one reactant contains at least one Si(CH3)2 group in its molecular structure, and the other reactant contains at least one -CF3 group in its molecular structure. The reactants are chemically combined in a solvent medium to form a solution of a high molecular weight polyamic acid, which is then converted to the corresponding polyimide.

Aromatic polyimides containing a dimethylsilane-linked dianhydride

NASA Technical Reports Server (NTRS)

St. Clair, Anne K. (Inventor); St. Clair, Terry L. (Inventor); Pratt, J. Richard (Inventor)

1992-01-01

A high-temperature stable, optically transparent, low dielectric aromatic polyimide is prepared by chemically combining equimolar quantities of an aromatic dianhydride reactant and an aromatic diamine reactant, which are selected so that one reactant contains at least one Si(CH.sub.3).sub.2 group in its molecular structure, and the other reactant contains at least one --CH.sub.3 group in its molecular structure. The reactants are chemically combined in a solvent medium to form a solution of a high molecular weight polyamic acid, which is then converted to the corresponding polyimide.

Detection of chlorinated aromatic compounds

DOEpatents

Ekechukwu, Amy A.

1996-01-01

A method for making a composition for measuring the concentration of chloated aromatic compounds in aqueous fluids, and an optical probe for use with the method. The composition comprises a hydrophobic polymer matrix, preferably polyamide, with a fluorescent indicator uniformly dispersed therein. The indicator fluoresces in the presence of the chlorinated aromatic compounds with an intensity dependent on the concentration of these compounds in the fluid of interest, such as 8-amino-2-naphthalene sulfonate. The probe includes a hollow cylindrical housing that contains the composition in its distal end. The probe admits an aqueous fluid to the probe interior for exposure to the composition. An optical fiber transmits excitation light from a remote source to the composition while the indicator reacts with chlorinated aromatic compounds present in the fluid. The resulting fluorescence light signal is reflected to a second optical fiber that transmits the light to a spectrophotometer for analysis.

40 CFR 721.5762 - Aromatic aldehyde phenolic resin (generic).

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 31 2011-07-01 2011-07-01 false Aromatic aldehyde phenolic resin... Specific Chemical Substances § 721.5762 Aromatic aldehyde phenolic resin (generic). (a) Chemical substance... aromatic aldehyde phenolic resin (PMN P-01-573) is subject to reporting under this section for the...

40 CFR 721.5762 - Aromatic aldehyde phenolic resin (generic).

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 32 2012-07-01 2012-07-01 false Aromatic aldehyde phenolic resin... Specific Chemical Substances § 721.5762 Aromatic aldehyde phenolic resin (generic). (a) Chemical substance... aromatic aldehyde phenolic resin (PMN P-01-573) is subject to reporting under this section for the...

40 CFR 721.5762 - Aromatic aldehyde phenolic resin (generic).

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 31 2014-07-01 2014-07-01 false Aromatic aldehyde phenolic resin... Specific Chemical Substances § 721.5762 Aromatic aldehyde phenolic resin (generic). (a) Chemical substance... aromatic aldehyde phenolic resin (PMN P-01-573) is subject to reporting under this section for the...

40 CFR 721.5762 - Aromatic aldehyde phenolic resin (generic).

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 32 2013-07-01 2013-07-01 false Aromatic aldehyde phenolic resin... Specific Chemical Substances § 721.5762 Aromatic aldehyde phenolic resin (generic). (a) Chemical substance... aromatic aldehyde phenolic resin (PMN P-01-573) is subject to reporting under this section for the...

40 CFR 721.5762 - Aromatic aldehyde phenolic resin (generic).

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 30 2010-07-01 2010-07-01 false Aromatic aldehyde phenolic resin... Specific Chemical Substances § 721.5762 Aromatic aldehyde phenolic resin (generic). (a) Chemical substance... aromatic aldehyde phenolic resin (PMN P-01-573) is subject to reporting under this section for the...

A hydroxycinnamoyltransferase responsible for synthesizing suberin aromatics in Arabidopsis

PubMed Central

Gou, Jin-Ying; Yu, Xiao-Hong; Liu, Chang-Jun

2009-01-01

Suberin, a polyester polymer in the cell wall of terrestrial plants, controls the transport of water and nutrients and protects plant from pathogenic infections and environmental stresses. Structurally, suberin consists of aliphatic and aromatic domains; p-hydroxycinnamates, such as ferulate, p-coumarate, and/or sinapate, are the major phenolic constituents of the latter. By analyzing the “wall-bound” phenolics of mutant lines of Arabidopsis deficient in a family of acyl-CoA dependent acyltransferase (BAHD) genes, we discovered that the formation of aromatic suberin in Arabidopsis, primarily in seed and root tissues, depends on a member of the BAHD superfamily of enzymes encoded by At5g41040. This enzyme exhibits an ω-hydroxyacid hydroxycinnamoyltransferase activity with an in vitro kinetic preference for feruloyl-CoA and 16-hydroxypalmitic acid. Knocking down or knocking out the At5g41040 gene in Arabidopsis reduces specifically the quantity of ferulate in suberin, but does not affect the accumulation of p-coumarate or sinapate. The loss of the suberin phenolic differentially affects the aliphatic monomer loads and alters the permeability and sensitivity of seeds and roots to salt stress. This highlights the importance of suberin aromatics in the polymer's function. PMID:19846769

Dermal exposure to jet fuel suppresses delayed-type hypersensitivity: a critical role for aromatic hydrocarbons.

PubMed

Ramos, Gerardo; Limon-Flores, Alberto Yairh; Ullrich, Stephen E

2007-12-01

Dermal exposure to military (JP-8) and/or commercial (Jet-A) jet fuel suppresses cell-mediated immune reactions. Immune regulatory cytokines and biological modifiers, including platelet activating factor (PAF), prostaglandin E(2), and interleukin-10, have been implicated in the pathway of events leading to immune suppression. It is estimated that approximately 260 different hydrocarbons are found in jet fuel, and the exact identity of the active immunotoxic agent(s) is unknown. The recent availability of synthetic jet fuel (S-8), which is refined from natural gas, and is devoid of aromatic hydrocarbons, made it feasible to design experiments to address this problem. Here we tested the hypothesis that the aromatic hydrocarbons present in jet fuel are responsible for immune suppression. We report that applying S-8 to the skin of mice does not upregulate the expression of epidermal cyclooxygenase-2 (COX-2) nor does it induce immune suppression. Adding back a cocktail of seven of the most prevalent aromatic hydrocarbons found in jet fuel (benzene, toluene, ethylbenzene, xylene, 1,2,4-trimethlybenzene, cyclohexylbenzene, and dimethylnaphthalene) to S-8 upregulated epidermal COX-2 expression and suppressed a delayed-type hypersensitivity (DTH) reaction. Injecting PAF receptor antagonists, or a selective cycloozygenase-2 inhibitor into mice treated with S-8 supplemented with the aromatic cocktail, blocked suppression of DTH, similar to data previously reported using JP-8. These findings identify the aromatic hydrocarbons found in jet fuel as the agents responsible for suppressing DTH, in part by the upregulation of COX-2, and the production of immune regulatory factors and cytokines.

10 CFR 63.16 - Review of site characterization activities. 2

Code of Federal Regulations, 2012 CFR

2012-01-01

... which such activities are carried out and to observe excavations, borings, and in situ tests, as they... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of site characterization activities. 2 2 In addition to the review of site characterization activities...

10 CFR 63.16 - Review of site characterization activities. 2

Code of Federal Regulations, 2011 CFR

2011-01-01

... which such activities are carried out and to observe excavations, borings, and in situ tests, as they... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of site characterization activities. 2 2 In addition to the review of site characterization activities...

10 CFR 63.16 - Review of site characterization activities. 2

Code of Federal Regulations, 2013 CFR

2013-01-01

... which such activities are carried out and to observe excavations, borings, and in situ tests, as they... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of site characterization activities. 2 2 In addition to the review of site characterization activities...

10 CFR 63.16 - Review of site characterization activities. 2

Code of Federal Regulations, 2010 CFR

2010-01-01

... which such activities are carried out and to observe excavations, borings, and in situ tests, as they... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of site characterization activities. 2 2 In addition to the review of site characterization activities...

10 CFR 63.16 - Review of site characterization activities. 2

Code of Federal Regulations, 2014 CFR

2014-01-01

... which such activities are carried out and to observe excavations, borings, and in situ tests, as they... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of site characterization activities. 2 2 In addition to the review of site characterization activities...

Aromatic VOCs global influence in the ozone production

NASA Astrophysics Data System (ADS)

Cabrera-Perez, David; Pozzer, Andrea

2016-04-01

Aromatic hydrocarbons are a subgroup of Volatile Organic Compounds (VOCs) of special interest in the atmosphere of urban and semi-urban areas. Aromatics form a high fraction of VOCs, are highly reactive and upon oxidation they are an important source of ozone. These group of VOCs are released to the atmosphere by processes related to biomass burning and fossil fuel consumption, while they are removed from the atmosphere primarily by OH reaction and by dry deposition. In addition, a branch of aromatics (ortho-nitrophenols) produce HONO upon photolysis, which is responsible of certain amount of the OH recycling. Despite their importance in the atmosphere in anthropogenic polluted areas, the influence of aromatics in the ozone production remains largely unknown. This is of particular relevance, being ozone a pollutant with severe side effects on air quality, health and climate. In this work the atmospheric impacts at global scale of the most emitted aromatic VOCs in the gas phase (benzene, toluene, xylenes, ethylbenzene, styrene, phenol, benzaldehyde and trimethylbenzenes) are analysed and assessed. Specifically, the impact on ozone due to aromatic oxidation is estimated, as this is of great interest in large urban areas and can be helpful for developing air pollution control strategies. Further targets are the quantification of the NOx loss and the OH recycling due to aromatic oxidation. In order to investigate these processes, two simulations were performed with the numerical chemistry and climate simulation ECHAM/MESSy Atmospheric Chemistry (EMAC) model. The simulations compare two cases, one with ozone concentrations when aromatics are present or the second one when they are missing. Finally, model simulated ozone is compared against a global set of observations in order to better constrain the model accuracy.

Recent Advances in Microbial Production of Aromatic Chemicals and Derivatives.

PubMed

Noda, Shuhei; Kondo, Akihiko

2017-08-01

Along with the development of metabolic engineering and synthetic biology tools, various microbes are being used to produce aromatic chemicals. In microbes, aromatics are mainly produced via a common important precursor, chorismate, in the shikimate pathway. Natural or non-natural aromatics have been produced by engineering metabolic pathways involving chorismate. In the past decade, novel approaches have appeared to produce various aromatics or to increase their productivity, whereas previously, the targets were mainly aromatic amino acids and the strategy was deregulating feedback inhibition. In this review, we summarize recent studies of microbial production of aromatics based on metabolic engineering approaches. In addition, future perspectives and challenges in this research area are discussed. Copyright © 2017 Elsevier Ltd. All rights reserved.

Extraction of sediment-associated polycyclic aromatic hydrocarbons with granular activated carbon.

PubMed

Rakowska, M I; Kupryianchyk, D; Grotenhuis, T; Rijnaarts, H H M; Koelmans, A A

2013-02-01

Addition of activated carbon (AC) to sediments has been proposed as a method to reduce ecotoxicological risks of sediment-bound contaminants. The present study explores the effectiveness of granular AC (GAC) in extracting polycyclic aromatic hydrocarbon (PAH) from highly contaminated sediments. Four candidate GAC materials were screened in terms of PAH extraction efficiency using single-step 24-h GAC extractions, with traditional 24-h Tenax extraction as a reference. Subsequently, sorption of native PAHs to the best performing GAC 1240W (0.45-1.70 mm) was studied for sediment only and for GAC-sediment mixtures at different GAC-sediment weight ratios, using 76-µm polyoxymethylene (POM) passive samplers. Granular AC sorption parameters for PAHs were determined by subtracting the contribution of PAH sorption to sediment from PAH sorption to the GAC-sediment mixture. It appears that the binding of PAHs and the effectiveness of GAC to reduce sediment porewater concentrations were highly dependent on the GAC-sediment mixing ratio and hydrophobicity of the PAH. Despite the considerable fouling of GAC by organic matter and oil, 50 to 90% of the most available PAH was extracted by the GAC during a 28-d contact time, at a dose as low as 4%, which also is a feasible dose in field-scale applications aimed at cleaning the sediment by GAC addition and removal. Copyright © 2012 SETAC.

Chemical composition and antimicrobial activity of the essential oil from the edible aromatic plant Aristolochia delavayi.

PubMed

Li, Zhi-Jian; Njateng, Guy S S; He, Wen-Jia; Zhang, Hong-Xia; Gu, Jian-Long; Chen, Shan-Na; Du, Zhi-Zhi

2013-11-01

The essential oil obtained by hydrodistillation from the aerial parts of Aristolochia delavayi Franch. (Aristolochiaceae), a unique edible aromatic plant consumed by the Nakhi (Naxi) people in Yunnan, China, was investigated using GC/MS analysis. In total, 95 components, representing more than 95% of the oil composition, were identified, and the main constituents found were (E)-dec-2-enal (52.0%), (E)-dodec-2-enal (6.8%), dodecanal (3.35%), heptanal (2.88%), and decanal (2.63%). The essential oil showed strong inhibitory activity (96% reduction) of the production of bacterial volatile sulfide compounds (VSC) by Klebsiella pneumoniae, an effect that was comparable with that of the reference compound citral (91% reduction). Moreover, the antimicrobial activity of the essential oil and the isolated major compound against eight bacterial and six fungal strains were evaluated. The essential oil showed significant antibacterial activity against Providencia stuartii and Escherichia coli, with minimal inhibitory concentrations (MIC) ranging from 3.9 to 62.5 μg/ml. The oil also showed strong inhibitory activity against the fungal strains Trichophyton ajelloi, Trichophyton terrestre, Candida glabrata, Candida guilliermondii, and Cryptococcus neoformans, with MIC values ranging from 3.9 to 31.25 μg/ml, while (E)-dec-2-enal presented a lower antifungal activity than the essential oil. Copyright © 2013 Verlag Helvetica Chimica Acta AG, Zürich.

Analogs of solid nanoparticles as precursors of aromatic hydrocarbons

NASA Astrophysics Data System (ADS)

Gadallah, K. A. K.; Mutschke, H.; Jäger, C.

2013-06-01

Context. Aromatic =CH and C=C vibrational bands have been observed within shocked interstellar regions, indicating the presence of aromatic emission carriers such as PAHs, which may have been created from adjacent molecular cloud material by interaction with a shock front. Aims: We investigate the evolution of the aromatic =CH and C=C vibrational modes at 3.3 and 6.2 μm wavelength in heated HAC materials, PAHs and mixed PAHs and HACs, respectively, aiming at an explanation of the evolution of carbonaceous dust grains in the shocked regions. Methods: Materials used in these analogs (HAC and PAH materials) were prepared by the laser ablation and the laser pyrolysis methods, respectively. The transmission electron microscopy (TEM) in high-resolution mode was used as an analytical technique to characterize the aromatic layers in HACs. Spectroscopic analysis was prformed in the mid-IR range. Results: A remarkable destruction of aliphatic structures in HACs has been observed with the thermal processing, while aromatic structures become dominating by increasing the diameters of the graphene layers. The aromatic bands at 3.3 and 6.2 μm, observed in the laboratory spectra of PAHs and of the combination of the PAHs and HAC materials, are also clearly observed in the spectrum of the heated HACs. These bands agree with those of aromatic bands observed in astronomical observations. Conclusions: Aromatization of HACs could be a pre-stage in the decomposition process of hydrocarbons that form PAH-clusters in such hot interstellar medium.

Mechanism for Ring-Opening of Aromatic Polymers by Remote Atmospheric Pressure Plasma

NASA Astrophysics Data System (ADS)

Gonzalez, Eleazar; Barankin, Michael; Guschl, Peter; Hicks, Robert

2009-10-01

A low-temperature, atmospheric pressure oxygen and helium plasma was used to treat the surfaces of polyetheretherketone, polyphenylsulfone, polyethersulfone, and polysulfone. These aromatic polymers were exposed to the afterglow of the plasma, which contained oxygen atoms, and to a lesser extent metastable oxygen (^1δg O2) and ozone. After less than 2.5 seconds treatment, the polymers were converted from a hydrophobic state with a water contact angle of 85±5 to a hydrophilic state with a water contact angle of 13±5 . It was found that plasma activation increased the bond strength to adhesives by as much as 4 times. X-ray photoelectron spectroscopy revealed that between 7% and 27% of the aromatic carbon atoms on the polymer surfaces was oxidized and converted into aldehyde and carboxylic acid groups. Analysis of polyethersulfone by internal reflection infrared spectroscopy showed that a fraction of the aromatic carbon atoms were transformed into C=C double bonds, ketones, and carboxylic acids after plasma exposure. It was concluded that the oxygen atoms generated by the atmospheric pressure plasma insert into the double bonds on the aromatic rings, forming a 3-member epoxy ring, which subsequently undergoes ring opening and oxidation to yield an aldehyde and a carboxylic acid group.

Molecular Biology of Anaerobic Aromatic Biodegradation.

DTIC Science & Technology

1992-08-14

manipulate and clone genes for aromatic acid degradation from the bacterium, Rhodopseudomonas palustris . These tools have enabled us to identify genes...anaerobic degradation of two selected aromatic acids - benzoate and 4-hydroxybenzoate - by one bacterial species - Rhodopseudomonas palustris . Our...PUBLICATIONS. Papers: Gibson, J., J. F. Geissler, and C. S. Harwood. 1990. Benzoate-coenzyme A ligase from Rhodopseudomonas palustris . Methods in Enzymology

Extraction of Lanthanide and Actinide Ions from Aqueous Mixtures Using a Carboxylic Acid-Functionalized Porous Aromatic Framework

DOE PAGES

Demir, Selvan; Brune, Nicholas K.; Van Humbeck, Jeffrey F.; ...

2016-04-08

Porous aromatic frameworks (PAFs) incorporating a high concentration of acid functional groups possess characteristics that are promising for use in separating lanthanide and actinide metal ions, as required in the treatment of radioactive waste. These materials have been shown to be indefinitely stable to concentrated acids and bases, potentially allowing for multiple adsorption/stripping cycles. Additionally, the PAFs combine exceptional features from MOFs and inorganic/ activated carbons giving rise to tunable pore surfaces and maximum chemical stability. Herein, we present a study of the adsorption of selected metal ions, Sr 2+, Fe 3+, Nd 3+, and Am 3+, from aqueous solutionsmore » employing a carbon-based porous aromatic framework, BPP-7 (Berkeley Porous Polymer-7). This material displays high metal loading capacities together with excellent adsorption selectivity for neodymium over strontium based on Langmuir adsorption isotherms and ideal adsorbed solution theory (IAST) calculations. Based in part upon X-ray absorption spectroscopy studies, the stronger adsorption of neodymium is attributed to multiple metal ion and binding site interactions resulting from the densely functionalized and highly interpenetrated structure of BPP-7. Finally, recyclability and combustibility experiments demonstrate that multiple adsorption/stripping cycles can be completed with minimal degradation of the polymer adsorption capacity.« less

Extraction of Lanthanide and Actinide Ions from Aqueous Mixtures Using a Carboxylic Acid-Functionalized Porous Aromatic Framework

PubMed Central

2016-01-01

Porous aromatic frameworks (PAFs) incorporating a high concentration of acid functional groups possess characteristics that are promising for use in separating lanthanide and actinide metal ions, as required in the treatment of radioactive waste. These materials have been shown to be indefinitely stable to concentrated acids and bases, potentially allowing for multiple adsorption/stripping cycles. Additionally, the PAFs combine exceptional features from MOFs and inorganic/activated carbons giving rise to tunable pore surfaces and maximum chemical stability. Herein, we present a study of the adsorption of selected metal ions, Sr2+, Fe3+, Nd3+, and Am3+, from aqueous solutions employing a carbon-based porous aromatic framework, BPP-7 (Berkeley Porous Polymer-7). This material displays high metal loading capacities together with excellent adsorption selectivity for neodymium over strontium based on Langmuir adsorption isotherms and ideal adsorbed solution theory (IAST) calculations. Based in part upon X-ray absorption spectroscopy studies, the stronger adsorption of neodymium is attributed to multiple metal ion and binding site interactions resulting from the densely functionalized and highly interpenetrated structure of BPP-7. Recyclability and combustibility experiments demonstrate that multiple adsorption/stripping cycles can be completed with minimal degradation of the polymer adsorption capacity. PMID:27163056

Polynuclear aromatic hydrocarbon analysis using the synchronous scanning luminoscope

NASA Astrophysics Data System (ADS)

Hyfantis, George J., Jr.; Teglas, Matthew S.; Wilbourn, Robert G.

2001-02-01

12 The Synchronous Scanning Luminoscope (SSL) is a field- portable, synchronous luminescence spectrofluorometer that was developed for on-site analysis of contaminated soil and ground water. The SSL is capable of quantitative analysis of total polynuclear aromatic hydrocarbons (PAHs) using phosphorescence and fluorescence techniques with a high correlation to laboratory data as illustrated by this study. The SSL is also capable of generating benzo(a)pyrene equivalency results, based on seven carcinogenic PAHs and Navy risk numbers, with a high correlation to laboratory data as illustrated by this study. These techniques allow rapid field assessments of total PAHs and benzo(a)pyrene equivalent concentrations. The Luminoscope is capable of detecting total PAHs to the parts per billion range. This paper describes standard field methods for using the SSL and describes the results of field/laboratory testing of PAHs. SSL results from two different hazardous waste sites are discussed.

Detection of chlorinated aromatic compounds

DOEpatents

Ekechukwu, A.A.

1996-02-06

A method for making a composition for measuring the concentration of chlorinated aromatic compounds in aqueous fluids, and an optical probe for use with the method are disclosed. The composition comprises a hydrophobic polymer matrix, preferably polyamide, with a fluorescent indicator uniformly dispersed therein. The indicator fluoresces in the presence of the chlorinated aromatic compounds with an intensity dependent on the concentration of these compounds in the fluid of interest, such as 8-amino-2-naphthalene sulfonate. The probe includes a hollow cylindrical housing that contains the composition in its distal end. The probe admits an aqueous fluid to the probe interior for exposure to the composition. An optical fiber transmits excitation light from a remote source to the composition while the indicator reacts with chlorinated aromatic compounds present in the fluid. The resulting fluorescence light signal is reflected to a second optical fiber that transmits the light to a spectrophotometer for analysis. 5 figs.

Air quality modeling of selected aromatic and non-aromatic air toxics in the Houston urban and industrial airshed

NASA Astrophysics Data System (ADS)

Coarfa, Violeta Florentina

2007-12-01

Air toxics, also called hazardous air pollutants (HAPs), pose a serious threat to human health and the environment. Their study is important in the Houston area, where point sources, mostly located along the Ship Channel, mobile and area sources contribute to large emissions of such toxic pollutants. Previous studies carried out in this area found dangerous levels of different HAPs in the atmosphere. This thesis presents several studies that were performed for the aromatic and non-aromatic air toxics in the HGA. For these studies we developed several tools: (1) a refined chemical mechanism, which explicitly represents 18 aromatic air toxics that were lumped under two model species by the previous version, based on their reactivity with the hydroxyl radical; (2) an engineering version of an existing air toxics photochemical model that enables us to perform much faster long-term simulations compared to the original model, that leads to a 8--9 times improvement in the running time across different computing platforms; (3) a combined emission inventory based on the available emission databases. Using the developed tools, we quantified the mobile source impact on a few selected air toxics, and analyzed the temporal and spatial variation of selected aromatic and non-aromatic air toxics in a few regions within the Houston area; these regions were characterized by different emissions and environmental conditions.

Watershed-based sources of polycyclic aromatic hydrocarbons in urban storm water.

PubMed

Stein, Eric D; Tiefenthaler, Liesl L; Schiff, Kenneth

2006-02-01

Polycyclic aromatic hydrocarbons (PAHs) are carcinogenic and mutagenic compounds, ubiquitous in the air and water of urban environments, and have been shown to accumulate in coastal estuarine and marine sediments. Although previous studies have documented concentrations and loads of PAHs in urban runoff, little is known about the sources and temporal patterns of PAH loading from storm water. This study characterized the sources and temporal patterns of PAHs in urban storm water by analyzing PAH concentrations and loads from a range of homogeneous land use sites and in-river mass emission sites throughout the greater Los Angeles, California, USA, region. Samples were collected at 30- to 60-min intervals over the course of a storm during multiple storm events over a four-year period in order to investigate PAH sources and inter- and intrastorm patterns in loading. Polycyclic aromatic hydrocarbon storm fluxes ranged from 1.3 g/km2 for the largely undeveloped Arroyo Sequit watershed to 223.7 g/km2 for the highly urbanized Verdugo Wash watershed, with average storm fluxes being 46 times higher in developed versus undeveloped watersheds. Early-season storms repeatedly produced substantially higher loads than comparably sized late-season storms. Within individual storms, PAHs exhibited a moderate first flush with between 30 and 60% of the total PAH load being discharged in the first 20% of the storm volume. The relative distribution of individual PAHs demonstrated a consistent predominance of high-molecular-weight compounds indicative of pyrogenic sources.

Computer simulation of the active site of human serum cholinesterase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kefang Jiao; Song Li; Zhengzheng Lu

1996-12-31

The first 3D-structure of acetylchelinesterase from Torpedo California electric organ (T.AChE) was published by JL. Sussman in 1991. We have simulated 3D-structure of human serum cholinesterase (H.BuChE) and the active site of H.BuChE. It is discovered by experiment that the residue of H.BuChE is still active site after a part of H.BuChE is cut. For example, the part of 21KD + 20KD is active site of H.BuChE. The 20KD as it is. Studies on these peptides by Hemelogy indicate that two active peptides have same negative electrostatic potential maps diagram. These negative electrostatic areas attached by acetyl choline with positivemore » electrostatic potency. We predict that 147...236 peptide of AChE could be active site because it was as 20KD as with negative electrostatic potential maps. We look forward to proving from other ones.« less

Device for aqueous detection of nitro-aromatic compounds

DOEpatents

Reagen, W.K.; Schulz, A.L.; Ingram, J.C.; Lancaster, G.D.; Grey, A.E.

1994-04-26

This invention relates to a compact and portable detection apparatus for nitro-aromatic based chemical compounds, such as nitrotoluenes, dinitrotoluenes, and trinitrotoluene (TNT). The apparatus is based upon the use of fiber optics using filtered light. The preferred process of the invention relies upon a reflective chemical sensor and optical and electronic components to monitor a decrease in fluorescence when the nitro-aromatic molecules in aqueous solution combine and react with a fluorescent polycyclic aromatic compound. 4 figures.

Device for aqueous detection of nitro-aromatic compounds

DOEpatents

Reagen, William K.; Schulz, Amber L.; Ingram, Jani C.; Lancaster, Gregory D.; Grey, Alan E.

1994-01-01

This invention relates to a compact and portable detection apparatus for ro-aromatic based chemical compounds, such as nitrotoluenes, dinitrotoluenes, and trinitrotoluene (TNT). The apparatus is based upon the use of fiber optics using filtered light. The preferred process of the invention relies upon a reflective chemical sensor and optical and electronic components to monitor a decrease in fluorescence when the nitro-aromatic molecules in aqueous solution combine and react with a fluorescent polycyclic aromatic compound.

Evidence for behavioral attractiveness of methoxylated aromatics in a dynastid scarab beetle-pollinated araceae.

PubMed

Dötterl, Stefan; David, Anja; Boland, Wilhelm; Silberbauer-Gottsberger, Ilse; Gottsberger, Gerhard

2012-12-01

Many plants attract their pollinators with floral scents, and these olfactory signals are especially important at night, when visual signals become inefficient. Dynastid scarab beetles are a speciose group of night-active pollinators, and several plants pollinated by these insects have methoxylated aromatic compounds in their scents. However, there is a large gap in our knowledge regarding the compounds responsible for beetle attraction. We used chemical analytical analyses to determine temporal patterns of scent emission and the composition of scent released from inflorescences of Philodendron selloum. The attractiveness of the main components in the scent to the dynastid scarab beetle Erioscelis emarginata, the exclusive pollinator of this plant, was assessed in field biotests. The amount of scent increased rapidly in the evening, and large amounts of scent were released during the activity time of the beetle pollinators. Inflorescences emitted a high number of compounds of different biosynthetic origin, among them both uncommon and also widespread flower scents. Methoxylated aromatic compounds dominated the scent, and 4-methoxystyrene, the most abundant compound, attracted E. emarginata beetles. Other compounds, such as (Z)-jasmone and possibly also the methoxylated aromatic compound 3,4-dimethoxystyrene increased the attractiveness of 4-methoxystyrene. Methoxylated aromatics, which are known from other dynastid pollinated plants as well, are important signals in many scarab beetles in a different context (e.g., pheromones), thus suggesting that these plants exploit pre-existing preferences of the beetles for attracting this group of insects as pollinators.

A NOVEL METABOLIC ACTIVATION PATHWAY FOR POLYCYCLIC AROMATIC HYDROCARBONS: REACTIVE OXYGEN SPECIES-MEDIATED DNA DAMAGE AND MORPHOLOGICAL CELL TRANSFORMATION IN MOUSE EMBRYO CELLS BY K-REGION DIOL METABOLITES

EPA Science Inventory

Benzo[ a ]pyrene (BP) is a well-studied polycyclic aromatic hydrocarbon (P AH) .Many
mechanisms have been suggested to explain its carcinogenic activity, yet many questions still
remain. K-region dihydrodiols (diols) ofPAHs are common metabolites and some are genotoxic. W...

Effects of halogenated aromatics/aliphatics and nitrogen(N)-heterocyclic aromatics on estimating the persistence of future pharmaceutical compounds using a modified QSAR model.

PubMed

Lim, Seung Joo; Fox, Peter

2014-02-01

The effects of halogenated aromatics/aliphatics and nitrogen(N)-heterocyclic aromatics on estimating the persistence of future pharmaceutical compounds were investigated using a modified half life equation. The potential future pharmaceutical compounds investigated were approximately 2000 pharmaceutical drugs currently undergoing the United States Food and Drug Administration (US FDA) testing. EPI Suite (BIOWIN) model estimates the fates of compounds based on the biodegradability under aerobic conditions. While BIOWIN considered the biodegradability of a compound only, the half life equation used in this study was modified by biodegradability, sorption and cometabolic oxidation. It was possible that the potential future pharmaceutical compounds were more accurately estimated using the modified half life equation. The modified half life equation considered sorption and cometabolic oxidation of halogenated aromatic/aliphatics and nitrogen(N)-heterocyclic aromatics in the sub-surface, while EPI Suite (BIOWIN) did not. Halogenated aliphatics in chemicals were more persistent than halogenated aromatics in the sub-surface. In addition, in the sub-surface environment, the fates of organic chemicals were much more affected by halogenation in chemicals than by nitrogen(N)-heterocyclic aromatics. © 2013.

De novo active sites for resurrected Precambrian enzymes

NASA Astrophysics Data System (ADS)

Risso, Valeria A.; Martinez-Rodriguez, Sergio; Candel, Adela M.; Krüger, Dennis M.; Pantoja-Uceda, David; Ortega-Muñoz, Mariano; Santoyo-Gonzalez, Francisco; Gaucher, Eric A.; Kamerlin, Shina C. L.; Bruix, Marta; Gavira, Jose A.; Sanchez-Ruiz, Jose M.

2017-07-01

Protein engineering studies often suggest the emergence of completely new enzyme functionalities to be highly improbable. However, enzymes likely catalysed many different reactions already in the last universal common ancestor. Mechanisms for the emergence of completely new active sites must therefore either plausibly exist or at least have existed at the primordial protein stage. Here, we use resurrected Precambrian proteins as scaffolds for protein engineering and demonstrate that a new active site can be generated through a single hydrophobic-to-ionizable amino acid replacement that generates a partially buried group with perturbed physico-chemical properties. We provide experimental and computational evidence that conformational flexibility can assist the emergence and subsequent evolution of new active sites by improving substrate and transition-state binding, through the sampling of many potentially productive conformations. Our results suggest a mechanism for the emergence of primordial enzymes and highlight the potential of ancestral reconstruction as a tool for protein engineering.

Antifungal and repellent activities of the essential oils from three aromatic herbs from western Himalaya

USDA-ARS?s Scientific Manuscript database

In this investigation we examined the essential oils of three aromatic plants; Zanthoxylum armatum, Juniperus communis, and, Dysphania ambrosioides, which are used by the local population of the western Himalayan region for medicinal purposes. These plants were studied for their antifungal, larvicid...

Polycyclic aromatic hydrocarbons residues in sandstorm depositions in Beijing, China

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fu, S.; Li, K.; Xia, X.J.

2009-02-15

This study was conducted to determine the concentration of 16 polycyclic aromatic hydrocarbons (PAHs) in sandstorm depositions in Beijing, China. The PAH concentrations in 13 samples collected in Beijing ranged from 0.18 to 3.52 {mu} g g{sup -1}. Analysis of the sources of contamination revealed that the PAHs were derived from a coal combustion source, although various effects of traffic emissions were also observed. Furthermore, the PAH levels in Beijing tended to be higher in the southeast. Finally, the Nemerow composite index revealed that the degree of pollution in the sandstorm depositions varied widely among sampling sites.

Concentration profiles, source apportionment and risk assessment of polycyclic aromatic hydrocarbons (PAHs) in dumpsite soils from Agbogbloshie e-waste dismantling site, Accra, Ghana.

PubMed

Daso, Adegbenro P; Akortia, Eric; Okonkwo, Jonathan O

2016-06-01

The concentrations of eighteen (18) polycyclic aromatic hydrocarbons (PAHs), including the 16 USEPA's priority PAHs as well as two alkyl-substituted naphthalenes were determined in dumpsite soils collected from different sampling sites within the Agbogbloshie e-waste dismantling site in Accra, Ghana. Following their isolation with ultrasonic-assisted extraction technique, the concentrations of the PAHs were determined by gas chromatography mass spectrometry (GC-MS). Loss-on-ignition (LOI) method was employed for the determination of total organic carbon (TOC) of the soil samples. The mean Σ18PAHs obtained were 3006, 5627, 3046, 5555, and 7199 ng g(-1) dry weight (dw) for sampling sites A (mosque), B (dismantling site), C (residential house/police station), D (personal computer repairers' shop) and E (e-waste open burning area), respectively. In all cases, the prevalence of phenanthrene, fluoranthene and pyrene was generally observed across the sampling sites. In this study, PAHs with two to three rings and four to six rings exhibited strong positive correlations, whereas BbF and BkF showed weak positive and negative correlations with other PAHs investigated. With the exception of BbF and BkF, all the PAHs had moderate to strong positive correlations with the TOC. Benzo[a]pyrene equivalent (BaPeq) concentration is a useful indicator of the carcinogenic potency of environmental matrices and these ranged between 111 and 454 ng g(-1), which are generally below the 'safe' level of 600 ng g(-1) established for the protection of the environment and human health. Interestingly, the seven carcinogenic PAHs were the major contributors to the BaPeq concentrations accounting between 97.7 and 98.3 %. Despite the minimal risk to cancer via exposure to the investigated dumpsite soil as indicated in the present study, the prolonged exposure to these pollutants via various exposure pathways may result in increased risk to cancer over time. The application of several

Heterogeneous Diels–Alder catalysis for biomass-derived aromatic compounds

DOE PAGES

Settle, Amy E.; Berstis, Laura; Rorrer, Nicholas A.; ...

2017-05-17

In this tutorial review, we provide an overview of heterogeneous Diels–Alder catalysis for the production of lignocellulosic biomass-derived aromatic compounds. Diels–Alder reactions afford an extremely selective and efficient route for carbon–carbon cycloadditions to produce intermediates that can readily undergo subsequent dehydration or dehydrogenation reactions for aromatization. As a result, catalysis of Diels–Alder reactions with biomass-derived dienes and dienophiles has seen a growth of interest in recent years; however, significant opportunities remain to (i) tailor heterogeneous catalyst materials for tandem Diels–Alder and aromatization reactions, and (ii) utilize biomass-derived dienes and dienophiles to access both conventional and novel aromatic monomers. As such,more » this review discusses the mechanistic aspects of Diels–Alder reactions from both an experimental and computational perspective, as well as the synergy of Brønsted–Lewis acid catalysts to facilitate tandem Diels–Alder and aromatization reactions. Heterogeneous catalyst design strategies for Diels–Alder reactions are reviewed for two exemplary solid acid catalysts, zeolites and polyoxometalates, and recent efforts for targeting direct replacement aromatic monomers from biomass are summarized. In conclusion, we point out important research directions for progressing Diels–Alder catalysis to target novel, aromatic monomers with chemical functionality that enables new properties compared to monomers that are readily accessible from petroleum.« less

Molecular dynamics explorations of active site structure in designed and evolved enzymes.

PubMed

Osuna, Sílvia; Jiménez-Osés, Gonzalo; Noey, Elizabeth L; Houk, K N

2015-04-21

This Account describes the use of molecular dynamics (MD) simulations to reveal how mutations alter the structure and organization of enzyme active sites. As proposed by Pauling about 70 years ago and elaborated by many others since then, biocatalysis is efficient when functional groups in the active site of an enzyme are in optimal positions for transition state stabilization. Changes in mechanism and covalent interactions are often critical parts of enzyme catalysis. We describe our explorations of the dynamical preorganization of active sites using MD, studying the fluctuations between active and inactive conformations normally concealed to static crystallography. MD shows how the various arrangements of active site residues influence the free energy of the transition state and relates the populations of the catalytic conformational ensemble to the enzyme activity. This Account is organized around three case studies from our laboratory. We first describe the importance of dynamics in evaluating a series of computationally designed and experimentally evolved enzymes for the Kemp elimination, a popular subject in the enzyme design field. We find that the dynamics of the active site is influenced not only by the original sequence design and subsequent mutations but also by the nature of the ligand present in the active site. In the second example, we show how microsecond MD has been used to uncover the role of remote mutations in the active site dynamics and catalysis of a transesterase, LovD. This enzyme was evolved by Tang at UCLA and Codexis, Inc., and is a useful commercial catalyst for the production of the drug simvastatin. X-ray analysis of inactive and active mutants did not reveal differences in the active sites, but relatively long time scale MD in solution showed that the active site of the wild-type enzyme preorganizes only upon binding of the acyl carrier protein (ACP) that delivers the natural acyl group to the active site. In the absence of bound ACP

Evaluation of the Significance of Starch Surface Binding Sites on Human Pancreatic α-Amylase.

PubMed

Zhang, Xiaohua; Caner, Sami; Kwan, Emily; Li, Chunmin; Brayer, Gary D; Withers, Stephen G

2016-11-01

Starch provides the major source of caloric intake in many diets. Cleavage of starch into malto-oligosaccharides in the gut is catalyzed by pancreatic α-amylase. These oligosaccharides are then further cleaved by gut wall α-glucosidases to release glucose, which is absorbed into the bloodstream. Potential surface binding sites for starch on the pancreatic amylase, distinct from the active site of the amylase, have been identified through X-ray crystallographic analyses. The role of these sites in the degradation of both starch granules and soluble starch was probed by the generation of a series of surface variants modified at each site to disrupt binding. Kinetic analysis of the binding and/or cleavage of substrates ranging from simple maltotriosides to soluble starch and insoluble starch granules has allowed evaluation of the potential role of each such surface site. In this way, two key surface binding sites, on the same face as the active site, are identified. One site, containing a pair of aromatic residues, is responsible for attachment to starch granules, while a second site featuring a tryptophan residue around which a malto-oligosaccharide wraps is shown to heavily influence soluble starch binding and hydrolysis. These studies provide insights into the mechanisms by which enzymes tackle the degradation of largely insoluble polymers and also present some new approaches to the interrogation of the binding sites involved.

Biodegradation of high-molecular-weight polycyclic aromatic hydrocarbons under anaerobic conditions: Overview of studies, proposed pathways and future perspectives.

PubMed

Nzila, Alexis

2018-05-07

The biodegradation of low- and high-molecular-weight polycyclic aromatic hydrocarbons (PAHs) (LWM-PAHs and HMW-PAHs, respectively) has been studied extensively under aerobic conditions. Molecular O 2 plays 2 critical roles in this biodegradation process. O 2 activates the aromatic rings through hydroxylation prior to ring opening and serves as a terminal electron acceptor (TEA). However, several microorganisms have devised ways of activating aromatic rings, leading to ring opening (and thus biodegradation) when TEAs other than O 2 are used (under anoxic conditions). These microorganisms belong to the sulfate-, nitrate-, and metal-ion-reducing bacteria and the methanogens. Although the anaerobic biodegradation of monocyclic aromatic hydrocarbons and LWM-PAH naphthalene have been studied, little information is available about the biodegradation of HMW-PAHs. This manuscript reviews studies of the anaerobic biodegradation of HMW-PAHs and identifies gaps that limit both our understanding and the efficiency of this biodegradation process. Strategies that can be employed to overcome these limitations are also discussed. Copyright © 2018 Elsevier Ltd. All rights reserved.

Relocating the Active-Site Lysine in Rhodopsin: 2. Evolutionary Intermediates.

PubMed

Devine, Erin L; Theobald, Douglas L; Oprian, Daniel D

2016-08-30

The visual pigment rhodopsin is a G protein-coupled receptor that covalently binds its retinal chromophore via a Schiff base linkage to an active-site Lys residue in the seventh transmembrane helix. Although this residue is strictly conserved among all type II retinylidene proteins, we found previously that the active-site Lys in bovine rhodopsin (Lys296) can be moved to three other locations (G90K, T94K, S186K) while retaining the ability to form a pigment with retinal and to activate transducin in a light-dependent manner [ Devine et al. ( 2013 ) Proc. Natl. Acad. Sci. USA 110 , 13351 - 13355 ]. Because the active-site Lys is not functionally constrained to be in helix seven, it is possible that it could relocate within the protein, most likely via an evolutionary intermediate with two active-site Lys. Therefore, in this study we characterized potential evolutionary intermediates with two Lys in the active site. Four mutant rhodopsins were prepared in which the original Lys296 was left untouched and a second Lys residue was substituted for G90K, T94K, S186K, or F293K. All four constructs covalently bind 11-cis-retinal, form a pigment, and activate transducin in a light-dependent manner. These results demonstrate that rhodopsin can tolerate a second Lys in the retinal binding pocket and suggest that an evolutionary intermediate with two Lys could allow migration of the Schiff base Lys to a position other than the observed, highly conserved location in the seventh TM helix. From sequence-based searches, we identified two groups of natural opsins, insect UV cones and neuropsins, that contain Lys residues at two positions in their active sites and also have intriguing spectral similarities to the mutant rhodopsins studied here.

1H NMR analysis of complexation of hydrotropic agents nicotinamide and caffeine with aromatic biologically active molecules in aqueous solution

NASA Astrophysics Data System (ADS)

Lantushenko, Anastasia O.; Mukhina, Yulia V.; Veselkov, Kyrill A.; Davies, David B.; Veselkov, Alexei N.

2004-07-01

NMR spectroscopy has been used to elucidate the molecular mechanism of solubilization action of hydrotropic agents nicotinamide (NA) and caffeine (CAF). Hetero-association of NA with riboflavine-mononucleotide (FMN) and CAF with low soluble in aqueous solution synthetic analogue of antibiotic actinomycin D, actinocyl-bis-(3-dimethylaminopropyl) amine (Actill), has been investigated by 500 MHz 1H NMR spectroscopy. Concentration and temperature dependences of proton chemical shifts have been analysed in terms of a statistical-thermodynamic model of indefinite self- and heteroassociation of aromatic molecules. The obtained results enable to conclude that NA-FMN and CAF-Actill intermolecular complexes are mainly stabilized by the stacking interactions of the aromatic chromophores. Hetero-association of the investigated molecules plays an important role in solubilization of aromatic drugs by hydrotropic agents nicotinamide and caffeine.

Effects of electronics, aromaticity, and solvent polarity on the rate of azaquinone-methide-mediated depolymerization of aromatic carbamate oligomers.

PubMed

Robbins, Jessica S; Schmid, Kyle M; Phillips, Scott T

2013-04-05

This paper uses physical-organic studies on well-defined oligomers to establish design principles for creating aromatic poly(carbamates) that depolymerize from head-to-tail in low dielectric constant environments when exposed to specific applied signals. We show that either increasing electron density or decreasing the aromaticity of aromatic repeating units in poly(carbamates) increase the overall depolymerization rate. For example, a methoxybenzene-based repeating unit provides depolymerization rates that are 143× faster than oligomers that contain a benzene-based repeating unit. Furthermore, the rate of depolymerization in the methoxybenzene-based system is tolerant to low dielectric environments, whereas the benzene-based oligomers are not.

Polycyclic Aromatic Hydrocarbons (PAHs) Mediate Transcriptional Activation of the ATP Binding Cassette Transporter ABCB6 Gene via the Aryl Hydrocarbon Receptor (AhR)*

PubMed Central

Chavan, Hemantkumar; Krishnamurthy, Partha

2012-01-01

Liver is endowed with a mechanism to induce hepatic cytochromes P450 (CYP450s) in response to therapeutic drugs and environmental contaminants, leading to increased detoxification and elimination of the xenobiotics. Each CYP450 is composed of an apoprotein moiety and a heme prosthetic group, which is required for CYP450 activity. Thus, under conditions of CYP450 induction, there is a coordinate increase in heme biosynthesis to compensate for the increased expression of CYP450s. ABCB6, a mitochondrial ATP binding cassette transporter, which regulates coproporphyrinogen transport from the cytoplasm into the mitochondria to complete heme biosynthesis, represents a previously unrecognized rate-limiting step in heme biosynthesis. However, it is not known if exposure to drugs and environmental contaminants induces ABCB6 expression, to assure an adequate and apparently coordinated supply of heme for the generation of functional cytochrome holoprotein. In the present study, we demonstrate that polycyclic aromatic hydrocarbons (PAHs), the widely distributed environmental toxicants shown to induce porphyrin accumulation causing hepatic porphyria, up-regulate ABCB6 expression in both mice and humans. Using siRNA technology and Abcb6 knock-out mice, we demonstrate that PAH-mediated increase in hepatic porphyrins is compromised in the absence of ABCB6. Moreover, in vivo studies in aryl hydrocarbon receptor (AhR) knock-out mice demonstrate that PAH induction of ABCB6 is mediated by AhR. Promoter activation studies combined with electrophoretic mobility shift assay and chromatin immunoprecipitation assay demonstrate direct interactions between the AhR binding sites in the ABCB6 promoter and the AhR receptor, implicating drug activation mechanisms for ABCB6 similar to those found in inducible cytochrome P450s. These studies are the first to describe direct transcriptional activation of both mouse and human ABCB6 by xenobiotics. PMID:22761424

Allosteric site-mediated active site inhibition of PBP2a using Quercetin 3-O-rutinoside and its combination.

PubMed

Rani, Nidhi; Vijayakumar, Saravanan; P T V, Lakshmi; Arunachalam, Annamalai

2016-08-01

Recent crystallographic study revealed the involvement of allosteric site in active site inhibition of penicillin binding protein (PBP2a), where one molecule of Ceftaroline (Cef) binds to the allosteric site of PBP2a and paved way for the other molecule (Cef) to bind at the active site. Though Cef has the potency to inhibit the PBP2a, its adverse side effects are of major concern. Previous studies have reported the antibacterial property of Quercetin derivatives, a group of natural compounds. Hence, the present study aims to evaluate the effect of Quercetin 3-o-rutinoside (Rut) in allosteric site-mediated active site inhibition of PBP2a. The molecular docking studies between allosteric site and ligands (Rut, Que, and Cef) revealed a better binding efficiency (G-score) of Rut (-7.790318) and Cef (-6.194946) with respect to Que (-5.079284). Molecular dynamic (MD) simulation studies showed significant changes at the active site in the presence of ligands (Rut and Cef) at allosteric site. Four different combinations of Rut and Cef were docked and their G-scores ranged between -6.320 and -8.623. MD studies revealed the stability of the key residue (Ser403) with Rut being at both sites, compared to other complexes. Morphological analysis through electron microscopy confirmed that combination of Rut and Cefixime was able to disturb the bacterial cell membrane in a similar fashion to that of Rut and Cefixime alone. The results of this study indicate that the affinity of Rut at both sites were equally good, with further validations Rut could be considered as an alternative for inhibiting MRSA growth.

Influence of active site location on catalytic activity in de novo-designed zinc metalloenzymes.

PubMed

Zastrow, Melissa L; Pecoraro, Vincent L

2013-04-17

While metalloprotein design has now yielded a number of successful metal-bound and even catalytically active constructs, the question of where to put a metal site along a linear, repetitive sequence has not been thoroughly addressed. Often several possibilities in a given sequence may exist that would appear equivalent but may in fact differ for metal affinity, substrate access, or protein dynamics. We present a systematic variation of active site location for a hydrolytically active ZnHis3O site contained within a de novo-designed three-stranded coiled coil. We find that the maximal rate, substrate access, and metal-binding affinity are dependent on the selected position, while catalytic efficiency for p-nitrophenyl acetate hydrolysis can be retained regardless of the location of the active site. This achievement demonstrates how efficient, tailor-made enzymes which control rate, pKa, substrate and solvent access (and selectivity), and metal-binding affinity may be realized. These findings may be applied to the more advanced de novo design of constructs containing secondary interactions, such as hydrogen-bonding channels. We are now confident that changes to location for accommodating such channels can be achieved without location-dependent loss of catalytic efficiency. These findings bring us closer to our ultimate goal of incorporating the secondary interactions we believe will be necessary in order to improve both active site properties and the catalytic efficiency to be competitive with the native enzyme, carbonic anhydrase.

Crude oil polycyclic aromatic hydrocarbons removal via clay-microbe-oil interactions: Effect of acid activated clay minerals.

PubMed

Ugochukwu, Uzochukwu C; Fialips, Claire I

2017-07-01

Acid treatment of clay minerals is known to modify their properties such as increase their surface area and surface acidity, making them suitable as catalysts in many chemical processes. However, the role of these surface properties during biodegradation processes of polycyclic aromatic hydrocarbons (PAHs) is only known for mild acid (0.5 M Hydrochloric acid) treated clays. Four different clay minerals were used for this study: a montmorillonite, a saponite, a palygorskite and a kaolinite. They were treated with 3 M hydrochloric acid to produce acid activated clay minerals. The role of the acid activated montmorillonite, saponite, palygorskite and kaolinite in comparison with the unmodified clay minerals in the removal of PAHs during biodegradation was investigated in microcosm experiments. The microcosm experiments contained micro-organisms, oil, and clays in aqueous medium with a hydrocarbon degrading microorganism community predominantly composed of Alcanivorax spp. Obtained results indicated that acid activated clays and unmodified kaolinite did not enhance the biodegradation of the PAHs whereas unmodified montmorillonite, palygorskite and saponite enhanced their biodegradation. In addition, unmodified palygorskite adsorbed the PAHs significantly due to its unique channel structure. Copyright © 2017 Elsevier Ltd. All rights reserved.

Remediation of petroleum hydrocarbon-contaminated sites by DNA diagnosis-based bioslurping technology.

PubMed

Kim, Seungjin; Krajmalnik-Brown, Rosa; Kim, Jong-Oh; Chung, Jinwook

2014-11-01

The application of effective remediation technologies can benefit from adequate preliminary testing, such as in lab-scale and Pilot-scale systems. Bioremediation technologies have demonstrated tremendous potential with regards to cost, but they cannot be used for all contaminated sites due to limitations in biological activity. The purpose of this study was to develop a DNA diagnostic method that reduces the time to select contaminated sites that are good candidates for bioremediation. We applied an oligonucleotide microarray method to detect and monitor genes that lead to aliphatic and aromatic degradation. Further, the bioremediation of a contaminated site, selected based on the results of the genetic diagnostic method, was achieved successfully by applying bioslurping in field tests. This gene-based diagnostic technique is a powerful tool to evaluate the potential for bioremediation in petroleum hydrocarbon contaminated soil. Copyright © 2014 Elsevier B.V. All rights reserved.

SOLAR RADIATION DOSE AND PHOTOTOXICITY OF POLYCYCLIC AROMATIC HYDROCARBONS: A CASE STUDY

EPA Science Inventory

The toxicity of polycyclic aromatic hydrocarbons increases by as much as three orders of magnitude in the presence of solar radiation. The risk of this photoactive toxicity is thus based on both tissue concentrations of potentially photo activated compounds and the levels of subs...

COMPUTATIONAL METHODS FOR STUDYING THE INTERACTION BETWEEN POLYCYCLIC AROMATIC HYDROCARBONS AND BIOLOGICAL MACROMOLECULES

EPA Science Inventory

Computational Methods for Studying the Interaction between Polycyclic Aromatic Hydrocarbons and Biological Macromolecules .

The mechanisms for the processes that result in significant biological activity of PAHs depend on the interaction of these molecules or their metabol...

Aromatic residues engineered into the beta-turn nucleation site of ubiquitin lead to a complex folding landscape, non-native side-chain interactions, and kinetic traps.

PubMed

Rea, Anita M; Simpson, Emma R; Meldrum, Jill K; Williams, Huw E L; Searle, Mark S

2008-12-02

The fast folding of small proteins is likely to be the product of evolutionary pressures that balance the search for native-like contacts in the transition state with the minimum number of stable non-native interactions that could lead to partially folded states prone to aggregation and amyloid formation. We have investigated the effects of non-native interactions on the folding landscape of yeast ubiquitin by introducing aromatic substitutions into the beta-turn region of the N-terminal beta-hairpin, using both the native G-bulged type I turn sequence (TXTGK) as well as an engineered 2:2 XNGK type I' turn sequence. The N-terminal beta-hairpin is a recognized folding nucleation site in ubiquitin. The folding kinetics for wt-Ub (TLTGK) and the type I' turn mutant (TNGK) reveal only a weakly populated intermediate, however, substitution with X = Phe or Trp in either context results in a high propensity to form a stable compact intermediate where the initial U-->I collapse is visible as a distinct kinetic phase. The introduction of Trp into either of the two host turn sequences results in either complex multiphase kinetics with the possibility of parallel folding pathways, or formation of a highly compact I-state stabilized by non-native interactions that must unfold before refolding. Sequence substitutions with aromatic residues within a localized beta-turn capable of forming non-native hydrophobic contacts in both the native state and partially folded states has the undesirable consequence that folding is frustrated by the formation of stable compact intermediates that evolutionary pressures at the sequence level may have largely eliminated.

Active Sites Environmental Monitoring Program: Mid-FY 1991 report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ashwood, T.L.; Wickliff, D.S.; Morrissey, C.M.

1991-10-01

This report summarizes the activities of the Active Sites Environmental Monitoring Program (ASEMP) from October 1990 through March 1991. The ASEMP was established in 1989 by Solid Waste Operations and the Environmental Sciences Division to provide early detection and performance monitoring at active low-level radioactive waste (LLW) disposal sites in Solid Waste Storage Area (SWSA) 6 and transuranic (TRU) waste storage sites in SWSA 5 as required by chapters II and III of US Department of Energy Order 5820.2A. Monitoring results continue to demonstrate the no LLW is being leached from the storage vaults on the tumulus pads. Loading ofmore » vaults on Tumulus II began during this reporting period and 115 vaults had been loaded by the end of March 1991.« less

New insights into thermal decomposition of polycyclic aromatic hydrocarbon oxyradicals.

PubMed

Liu, Peng; Lin, He; Yang, Yang; Shao, Can; Gu, Chen; Huang, Zhen

2014-12-04

Thermal decompositions of polycyclic aromatic hydrocarbon (PAH) oxyradicals on various surface sites including five-membered ring, free-edge, zigzag, and armchair have been systematically investigated by using ab initio density functional theory B3LYP/6-311+G(d,p) basis set. The calculation based on Hückel theory indicates that PAHs (3H-cydopenta[a]anthracene oxyradical) with oxyradicals on a five-membered ring site have high chemical reactivity. The rate coefficients of PAH oxyradical decomposition were evaluated by using Rice-Ramsperger-Kassel-Marcus theory and solving the master equations in the temperature range of 1500-2500 K and the pressure range of 0.1-10 atm. The kinetic calculations revealed that the rate coefficients of PAH oxyradical decomposition are temperature-, pressure-, and surface site-dependent, and the oxyradical on a five-membered ring is easier to decompose than that on a six-membered ring. Four-membered rings were found in decomposition of the five-membered ring, and a new reaction channel of PAH evolution involving four-membered rings is recommended.

Temporal dynamics of the arthropod community in pear orchards intercropped with aromatic plants.

PubMed

Beizhou, Song; Jie, Zhang; Jinghui, Hu; Hongying, Wu; Yun, Kong; Yuncong, Yao

2011-09-01

Increasing attention has been paid to enhancing biological control through habitat management in agricultural systems for enhanced pest management. Pest management benefits can be realised by intercropping, which can increase natural enemy abundance and, in turn, reduce pest abundance. In this study, the composition and temporal dynamics of arthropod communities in pear orchards when intercropped with aromatic plants were investigated, and the effectiveness and applicability of aromatic plants as intercrops for enhancing insect control were assessed. When compared with natural grasses or clean tillage, intercropping significantly reduced pest abundance and increased the ratio of natural enemies to pests. Intercropping also shortened the occurrence duration and depressed the incidence peak in annual dynamics curves of the pest subcommunity and the arthropod community, mainly because of the repellent effects of aromatic plants. Equally important, intercropping significantly reduced the numbers of major pests, such as Psylla chinensis, Aphis citricola and Pseudococcus comstocki, while their incidence period was delayed to varying degrees, and the numbers of their dominant natural enemies (Coccinella septempunctata, Phytoseiulus persimilis and Chrysoperla sinica) increased. Intercropping with aromatic plants led to a considerable improvement in arthropod pest management by enhancing the activity of the beneficial arthropod community within the pear orchard ecosystem. Copyright © 2011 Society of Chemical Industry.

The high-temperature oxidation of aromatic hydrocarbons

NASA Technical Reports Server (NTRS)

Brezinsky, K.

1986-01-01

Chemical mechanisms of the atmospheric pressure, high-temperature (875-1500 K) gas-phase oxidation of benzene, toluene, ethylbenzene, and propylbenzene are described and discussed. Oxidation trends evident from turbulent flow reactor experiments serve as the basis for the mechanisms of the oxidation of benzene and alkylated aromatics. The potential effects of very high temperatures and pressures on the chemistry of oxidation of aromatics are described. The oxidation of benzene and phenyl radical has been found to proceed in a stepwise C6-C5-C4 sequence. Species profiles obtained from flow-reactor experiments suggest that the oxidation of benzene and phenyl radical follows the generalized route via phenoxy, cyclopentadienyl and butadienyl radical. The oxidation of the C4 species branches into multiple pathways that yield copious amounts of ethylene and acetylene. Certain major trends are evident: the alkylated aromatics on initial attack either form styrene, benzyl radical or benzene. The styrene reacts further to produce a benzyl radical or benzene. The oxidation of an alkylated aromatic hydrocarbon appears eventually to reduce to the oxidation of either phenyl radical or benzene.

40 CFR 721.775 - Brominated aromatic com-pound (generic name).

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 30 2010-07-01 2010-07-01 false Brominated aromatic com-pound (generic... Specific Chemical Substances § 721.775 Brominated aromatic com-pound (generic name). (a) Chemical... as a brominated aromatic compound (PMN P-84-824) is subject to reporting under this section for the...

Associations between polycyclic aromatic hydrocarbon (PAH) exposure and oxidative stress in people living near e-waste recycling facilities in China.

PubMed

Lu, Shao-You; Li, Yan-Xi; Zhang, Jian-Qing; Zhang, Tao; Liu, Gui-Hua; Huang, Ming-Zhi; Li, Xiao; Ruan, Ju-Jun; Kannan, Kurunthachalam; Qiu, Rong-Liang

2016-09-01

Emission of polycyclic aromatic hydrocarbons (PAHs) from e-waste recycling activities in China is known. However, little is known on the association between PAH exposure and oxidative damage to DNA and lipid content in people living near e-waste dismantling sites. In this study, ten hydroxylated polycyclic aromatic hydrocarbons (OH-PAHs) and two biomarkers [8-hydroxy-2'-deoxyguanosine (8-OHdG) and malondialdehyde (MDA)] of oxidative stress were investigated in urine samples collected from people living in and around e-waste dismantling facilities, and in reference population from rural and urban areas in China. The urinary levels of ∑10OH-PAHs determined in e-waste recycling area (GM: 25.4μg/g Cre) were significantly higher (p<0.05) than those found in both rural (11.7μg/g Cre) and urban (10.9μg/g Cre) reference areas. The occupationally exposed e-waste workers (36.6μg/g Cre) showed significantly higher (p<0.01) urinary Σ10OH-PAHs concentrations than non-occupationally exposed people (23.2μg/g Cre) living in the e-waste recycling site. The differences in urinary Σ10OH-PAHs levels between smokers (23.4μg/g Cre) and non-smokers (24.7μg/g Cre) were not significant (p>0.05) in e-waste dismantling sites, while these differences were significant (p<0.05) in rural and urban reference areas; this indicated that smoking is not associated with elevated levels of PAH exposure in e-waste dismantling site. Furthermore, we found that urinary concentrations of Σ10OH-PAHs and individual OH-PAHs were significantly associated with elevated 8-OHdG, in samples collected from e-waste dismantling site; the levels of urinary 1-hydroxypyrene (1-PYR) (r=0.284, p<0.01) was significantly positively associated with MDA. Our results indicate that the exposure to PAHs at the e-waste dismantling site may have an effect on oxidative damage to DNA among selected participants, but this needs to be validated in large studies. Copyright © 2016 Elsevier Ltd. All rights reserved.

Antimicrobial Activity of Seven Essential Oils From Iranian Aromatic Plants Against Common Causes of Oral Infections

PubMed Central

Zomorodian, Kamiar; Ghadiri, Pooria; Saharkhiz, Mohammad Jamal; Moein, Mohammad Reza; Mehriar, Peiman; Bahrani, Farideh; Golzar, Tahereh; Pakshir, Keyvan; Fani, Mohammad Mehdi

2015-01-01

Background: Over the past two decades, there has been a growing trend in using oral hygienic products originating from natural resources such as essential oils (EOs) and plant extracts. Seven aromatic plants used in this study are among popular traditional Iranian medicinal plants with potential application in modern medicine as anti-oral infectious diseases. Objectives: This study was conducted to determine the chemical composition and antimicrobial activities of essential oils from seven medicinal plants against pathogens causing oral infections. Materials and Methods: The chemical compositions of EOs distilled from seven plants were analyzed by gas chromatography/mass spectrometry (GC/MS). These plants included Satureja khuzestanica, S. bachtiarica, Ocimum sanctum, Artemisia sieberi, Zataria multiflora, Carum copticum and Oliveria decumbens. The antimicrobial activity of the essential oils was evaluated by broth micro-dilution in 96 well plates as recommended by the Clinical and Laboratory Standards Institute (CLSI) methods. Results: The tested EOs inhibited the growth of examined oral pathogens at concentrations of 0.015-16 µL/mL. Among the examined oral pathogens, Enterococcus faecalis had the highest Minimum Inhibitory Concentrations (MICs) and Minimum Microbicidal Concentrations (MMCs). Of the examined EOs, S. khuzestanica, Z. multiflora and S. bachtiarica, showed the highest antimicrobial activities, respectively, while Artemisia sieberi exhibited the lowest antimicrobial activity. Conclusions: The excellent antimicrobial activities of the tested EOs might be due to their major phenolic or alcoholic monoterpenes with known antimicrobial activities. Hence, these EOs can be possibly used as an antimicrobial agent in treatment and control of oral pathogens. PMID:25793100

Valorization of essential oils from Moroccan aromatic plants.

PubMed

Santana, Omar; Fe Andrés, Maria; Sanz, Jesús; Errahmani, Naima; Abdeslam, Lamiri; González-Coloma, Azucena

2014-08-01

The chemical composition and biological activity of cultivated and wild medicinal and aromatic plants from Morocco (Artemisia herba-alba, Lippia citriodora, Mentha pulegium, M. spicata, Myrtus communis, Rosmarinus officinalis, and Thymus satureioides) are described. The essential oils (EOs) of these species have been analyzed by GC-MS. The antifeedant, nematicidal and phytotoxic activities of the EOs were tested on insect pests (Spodoptera littoralis, Myzus persicae and Rhopalosiphum padi), root-knot nematodes (Meloydogine javanica) and plants (Lactuca sativa, Lolium perenne and Lycopersicum esculentum). EOs from A. herba-alba, M. pulegium and R. officinalis were strong antifeedants against S. littoralis, M. persicae and R. padi. EOs from L. citriodora, M. spicata and T. satureioides showed high nematicidal activity. These biological effects are explained by the activity of the major EO components and/or synergistic effects.

[Polycyclic aromatic hydrocarbons (PAHs) in herbs and fruit teas].

PubMed

Ciemniak, Artur

2005-01-01

Polycyclic aromatic hydrocarbons (PAHs) of which benzo[a]pyrene is the most commonly studied and measured, are fused - ring aromatic compounds formed in both natural and man made processes and are found widely distributed throughout the human environment. PAHs occur as contaminants in different food categories and beverages including water, vegetables, fruit, cereals, oils and fats, barbecued and smoked meat. The sources of PAHs in food are predominantly from environmental pollution and food processing. PAHs emissions from automobile traffic and industry activities were show to influence the PAHs levels in vegetables and fruits. The present study was carried out to determine levels of 16 basic PAHs in herbs and fruit teas. The method was based on the hexane extraction and cleaned up by florisil cartridge. The extracts were analysed by GC-MS. The levels of total PAHs varied from 48,27 microg/kg (hibiscus tea) to 1703 microg/kg (green tea). The highest level of BaP was found in lime tea (74,2 microg/kg).

Aromatic Structure in Simulates Titan Aerosol

NASA Technical Reports Server (NTRS)

Trainer, Melissa G.; Loeffler, M. J.; Anderson, C. M.; Hudson, R. L.; Samuelson, R. E.; Moore, M. A.

2011-01-01

Observations of Titan by the Cassini Composite Infrared Spectrometer (CIRS) between 560 and 20 per centimeter (approximately 18 to 500 micrometers) have been used to infer the vertical variations of Titan's ice abundances, as well as those of the aerosol from the surface to an altitude of 300 km [1]. The aerosol has a broad emission feature centered approximately at 140 per centimeter (71 micrometers). As seen in Figure 1, this feature cannot be reproduced using currently available optical constants from laboratory-generated Titan aerosol analogs [2]. The far-IR is uniquely qualified for investigating low-energy vibrational motions within the lattice structures of COITIDlex aerosol. The feature observed by CIRS is broad, and does not likely arise from individual molecules, but rather is representative of the skeletal movements of macromolecules. Since Cassini's arrival at Titan, benzene (C6H6) has been detected in the atmosphere at ppm levels as well as ions that may be polycyclic aromatic hydrocarbons (PAHs) [3]. We speculate that the feature may be a blended composite that can be identified with low-energy vibrations of two-dimensional lattice structures of large molecules, such as PAHs or nitrogenated aromatics. Such structures do not dominate the composition of analog materials generated from CH4 and N2 irradiation. We are performing studies forming aerosol analog via UV irradiation of aromatic precursors - specifically C6H6 - to understand how the unique chemical architecture of the products will influence the observable aerosol characteristics. The optical and chemical properties of the aromatic analog will be compared to those formed from CH4/N2 mixtures, with a focus on the as-yet unidentified far-IR absorbance feature. Preliminary results indicate that the photochemically-formed aromatic aerosol has distinct chemical composition, and may incorporate nitrogen either into the ring structure or adjoined chemical groups. These compositional differences are

Effect of iodide on transformation of phenolic compounds by nonradical activation of peroxydisulfate in the presence of carbon nanotube: Kinetics, impacting factors, and formation of iodinated aromatic products.

PubMed

Guan, Chaoting; Jiang, Jin; Pang, Suyan; Luo, Congwei; Yang, Yi; Ma, Jun; Yu, Jing; Zhao, Xi

2018-06-04

Our recent study has demonstrated that iodide (I - ) can be easily and almost entirely oxidized to hypoiodous acid (HOI) but not to iodate by nonradical activation of peroxydisulfate (PDS) in the presence of a commercial carbon nanotube (CNT). In this work, the oxidation kinetics of phenolic compounds by the PDS/CNT system in the presence of I - were examined and potential formation of iodinated aromatic products was explored. Experimental results suggested that I - enhanced the transformation of six selected substituted phenols, primarily attributed to the generation of HOI that was considerably reactive toward these phenolic compounds. More significant enhancement was obtained at higher I - concentrations or lower pH values, while the change of PDS or CNT dosages exhibited a slight impact on the enhancing effect of I - . Product analyses with liquid chromatography tandem mass spectrometry clearly revealed the production of iodinated aromatic products when p-hydroxybenzoic acid (p-HBA, a model phenol) was treated by the PDS/CNT/I - system in both synthetic and real waters. Their formation pathways probably involved the substitution of HOI on aromatic ring of p-HBA, as well as the generation of iodinated p-HBA phenoxyl radicals and subsequent coupling of these radicals. Given the considerable toxicity and harmful effects of these iodinated aromatic products, particular attention should be paid when the novel PDS/CNT oxidation technology is applied for treatment of phenolic contaminants in iodide-containing waters. Copyright © 2018 Elsevier Ltd. All rights reserved.

Hemoglobin binding of aromatic amines: molecular dosimetry and quantitative structure-activity relationships for N-oxidation.

PubMed Central

Sabbioni, G

1993-01-01

Aromatic amines are important intermediates in industrial manufacturing. N-Oxidation to N-hydroxyarylamines is a key step in determining the genotoxic properties of aromatic amines. N-Hydroxyarylamines can form adducts with DNA, with tissue proteins, and with the blood proteins albumin and hemoglobin in a dose-dependent manner. The determination of hemoglobin adducts is a useful tool for biomonitoring exposed populations. We have established the hemoglobin binding index (HBI) [(mmole compound/mole hemoglobin)/(mmole compound/kg body weight)] of several aromatic amines in female Wistar rats. Including the values from other researchers obtained in the same rat strain, the logarithm of hemoglobin binding (logHBI) was plotted against the following parameters: the sum of the Hammett constants(sigma sigma = sigma p + sigma m), pKa, logP (octanol/water), the half-wave oxidation potential (E1/2), and the electronic descriptors of the amines and their corresponding nitrenium ions obtained by semi-empirical calculations (MNDO, AMI, and PM3), such as atomic charge densities, energies of the highest occupied molecular orbit and lowest occupied molecular orbit and their coefficients, the bond order of C-N, the dipole moments, and the reaction enthalpy [MNDOHF, AM1HF or PM3HF = Hf(nitrenium) - Hf(amine)]. The correlation coefficients were determined from the plots of all parameters against log HBI for all amines by means of linear regression analysis. The amines were classified in three groups: group 1, all parasubstituted amines (maximum, n = 9); group 2, all amines with halogens (maximun, n = 11); and group 3, all amines with alkyl groups (maximum, n = 13).(ABSTRACT TRUNCATED AT 250 WORDS) PMID:8319626

Self-assembled electrical materials from contorted aromatics

NASA Astrophysics Data System (ADS)

Xiao, Shengxiong

This thesis describes the design, synthesis, self-assembly and electrical properties of new types of contorted polycyclic aromatic hydrocarbons. These topologically interesting contorted aromatics show promising transistor characteristics as new building blocks for organic field-effect transistors (OFETs) at different length scales. In chapter 2, a class of pentacenes that are substituted along their long edges with aromatic rings were synthesized. Their solid-state assemblies were studied by X-ray crystallography. Their performance as thin film transistors (TFTs) and single crystal field effect transistors (SCFETs) were systematically evaluated. A structure-property relationship between these highly phenylated pentacenes was found. Chapter 3 explores the new concept of whether a non-planar aromatic core could yield efficacious electronic materials, as the ultimate success in the organic electronics will require a holistic approach to creating new building blocks. Synthesis, functionalization and assembly of a new type of contorted hexabenzocoronene (HBC) whose aromatic core is heavily distorted away from planarity due to the steric congestion around its proximal carbons were discussed. Structural studies by X-ray crystallography showed that these HBC molecules stack into columnar structures in the solid state, which are ideal for conduction. Chapter 4 describes that microscale liquid crystalline thin film OFETs of tetradodecyloxy HBC showed the best transistor properties of all discotic columnar materials. Chapter 5 details the fabrication and characterization of nanoscale single crystalline fiber OFETs of octadodecyloxyl HBC. In Chapter 6 we show that a molecular scale monolayer of HBC acid chlorides could be self-assembled on SiO2 insulating layer and could be organized laterally between the ends of 2 nm carbon nanotube gaps to form high quality FETs that act as environmental and chemical sensors. Chapter 7 details the enforced one-dimensional photoconductivity

Biosynthetically directed fractional 13C labeling facilitates identification of Phe and Tyr aromatic signals in proteins.

PubMed

Jacob, Jaison; Louis, John M; Nesheiwat, Issa; Torchia, Dennis A

2002-11-01

Analysis of 2D [(13)C,(1)H]-HSQC spectra of biosynthetic fractionally (13)C labeled proteins is a reliable, straightforward means to obtain stereospecific assignments of Val and Leu methyl sites in proteins. Herein we show that the same fractionally labeled protein sample facilitates observation and identification of Phe and Tyr aromatic signals. This is the case, in part, because the fractional (13)C labeling yields aromatic rings in which some of the (13)C-(13)C J-couplings, present in uniformly labeled samples, are absent. Also, the number of homonuclear J-coupling partners differs for the delta-, epsilon- and zeta-carbons. This enabled us to vary their signal intensities in distinctly different ways by appropriately setting the (13)C constant-time period in 2D [(13)C,(1)H]-HSQC spectra. We illustrate the application of this approach to an 18 kDa protein, c-VIAF, a modulator of apoptosis. In addition, we show that cancellation of the aromatic (13)C CSA and (13)C-(1)H dipolar interactions can be fruitfully utilized in the case of the fractionally labeled sample to obtain high resolution (13)C constant-time spectra with good sensitivity.

DIFFUSIVE EXCHANGE OF GASEOUS POLYCYCLIC AROMATIC HYDROCARBONS AND POLYCHLORINATED BIPHENYLS ACROSS THE AIR-WATER INTERFACE OF THE CHESAPEAKE BAY. (R825245)

EPA Science Inventory

Dissolved and gas-phase concentrations of nine polycyclic aromatic hydrocarbons and 46 polychlorinated biphenyl congeners were measured at eight sites on the Chesapeake Bay at four different times of the year to estimate net diffusive air-water gas exchange rates. Gaseous PAHs ar...

Antioxidant activity of a new aromatic geranyl derivative of the resinous exudates from Heliotropium glutinosum Phil.

PubMed

Modak, Brenda; Rojas, Macarena; Torres, René; Rodilla, Jesús; Luebert, Federico

2007-05-21

Heliotropium glutinosum Phil. (Heliotropiceae) is a resinous bush that grows at a height of 2000 m in Chañaral, Chile. From the resinous exudates of Heliotropium glutinosum Phil. a new aromatic geranyl derivative: 4-methoxy-3-[(2)-7'-methyl-3'-hydroxymethyl-2',6'-octadienyl] phenol (1) and three flavonoids: 5,3'-dihydroxy-7,4'-dimethoxyflavanone (2), 5,4'-dihydroxy-7-methoxyflavanone (3) and 4'-acetyl-5-hydroxy-7-methoxyflavanone (4) were isolated and their structures were determined. Their antioxidant activity were evaluated using the bleaching of ABTS and DPPH derived cation radical methods and expressed in terms of FRE (fast reacting equivalents) and TRE (total reacting equivalents), where FRE is a good measure of the quick protection of a given compound against oxidants and TRE measures the degree of long-term protection of the antioxidant, or how effective it is against a strong oxidative stress.

Intermolecular hydrogen bonds in hetero-complexes of biologically active aromatic molecules probed by the methods of vibrational spectroscopy

NASA Astrophysics Data System (ADS)

Semenov, M. A.; Blyzniuk, Iu. N.; Bolbukh, T. V.; Shestopalova, A. V.; Evstigneev, M. P.; Maleev, V. Ya.

2012-09-01

By the methods of vibrational spectroscopy (Infrared and Raman) the investigation of the hetero-association of biologically active aromatic compounds: flavin-mononucleotide (FMN), ethidium bromide (EB) and proflavine (PRF) was performed in aqueous solutions. It was shown that between the functional groups (Cdbnd O and NH2) the intermolecular hydrogen bonds are formed in the hetero-complexes FMN-EB and FMN-PRF, additionally stabilizing these structures. An estimation of the enthalpy of Н-bonding obtained from experimental shifts of carbonyl vibrational frequencies has shown that the H-bonds do not dominate in the magnitude of experimentally measured total enthalpy of the hetero-association reactions. The main stabilization is likely due to intermolecular interactions of the molecules in these complexes and their interaction with water environment.

Quantitative structure-activity relationships studies of CCR5 inhibitors and toxicity of aromatic compounds using gene expression programming.

PubMed

Shi, Weimin; Zhang, Xiaoya; Shen, Qi

2010-01-01

Quantitative structure-activity relationship (QSAR) study of chemokine receptor 5 (CCR5) binding affinity of substituted 1-(3,3-diphenylpropyl)-piperidinyl amides and ureas and toxicity of aromatic compounds have been performed. The gene expression programming (GEP) was used to select variables and produce nonlinear QSAR models simultaneously using the selected variables. In our GEP implementation, a simple and convenient method was proposed to infer the K-expression from the number of arguments of the function in a gene, without building the expression tree. The results were compared to those obtained by artificial neural network (ANN) and support vector machine (SVM). It has been demonstrated that the GEP is a useful tool for QSAR modeling. Copyright 2009 Elsevier Masson SAS. All rights reserved.

Sorption of Aromatic Compounds with Copolymer Sorbent Materials Containing β-Cyclodextrin.

PubMed

Wilson, Lee D; Mohamed, Mohamed H; Berhaut, Christopher L

2011-08-29

Urethane copolymer sorbent materials that incorporate β-cyclodextrin (CD) have been prepared and their sorption properties with chlorinated aromatic compounds (i.e., pentachlorophenol, 2,4-dichlorophenol and 2,4-dichlorophenoxy acetic acid) have been evaluated. The sorption properties of granular activated carbon (GAC) were similarly compared in aqueous solution at variable pH conditions. The sorbents displayed variable BET surface areas as follows: MDI-X copolymers (< 10¹ m²/g), CDI-X copolymers (< 10¹ m²/g), and granular activated carbon (GAC ~10³ m²/g). The sorption capacities for the copolymers sorbents are listed in descending order, as follows: GAC > CDI-3 copolymer ≈ MDI-3 copolymer. The sorption capacity for the aromatic adsorbates with each sorbent are listed in descending order, as follows: 2,4-dichlorophenol > 2,4-dichlorophenoxy acetic acid > pentachlorophenol. In general, the differences in the sorption properties of the copolymer sorbents with the chlorinated organics were related to the following factors: (i) surface area of the sorbent; (ii) CD content and accessibility; and (iii) and the chemical nature of the sorbent material.

Sorption of Aromatic Compounds with Copolymer Sorbent Materials Containing β-Cyclodextrin

PubMed Central

Wilson, Lee D.; Mohamed, Mohamed H.; Berhaut, Christopher L.

2011-01-01

Urethane copolymer sorbent materials that incorporate β-cyclodextrin (CD) have been prepared and their sorption properties with chlorinated aromatic compounds (i.e., pentachlorophenol, 2,4-dichlorophenol and 2,4-dichlorophenoxy acetic acid) have been evaluated. The sorption properties of granular activated carbon (GAC) were similarly compared in aqueous solution at variable pH conditions. The sorbents displayed variable BET surface areas as follows: MDI-X copolymers (< 101 m2/g), CDI-X copolymers (< 101 m2/g), and granular activated carbon (GAC ~103 m2/g). The sorption capacities for the copolymers sorbents are listed in descending order, as follows: GAC > CDI-3 copolymer ≈ MDI-3 copolymer. The sorption capacity for the aromatic adsorbates with each sorbent are listed in descending order, as follows: 2,4-dichlorophenol > 2,4-dichlorophenoxy acetic acid > pentachlorophenol. In general, the differences in the sorption properties of the copolymer sorbents with the chlorinated organics were related to the following factors: (i) surface area of the sorbent; (ii) CD content and accessibility; and (iii) and the chemical nature of the sorbent material. PMID:28824156

Dimethandrolone (7α,11β-dimethyl-19-nortestosterone) and 11β-methyl-19-nortestosterone are not converted to aromatic A-ring products in the presence of recombinant human aromatase☆

PubMed Central

Attardi, Barbara J.; Pham, Trung C.; Radler, Lisa M.; Burgenson, Janet; Hild, Sheri A.; Reel, Jerry R.

2008-01-01

Dimethandrolone undecanoate (DMAU: 7α,11β-dimethyl-19-nortestosterone 17β-undecanoate) is a potent orally active androgen in development for hormonal therapy in men. Cleavage of the 17β-ester bond by esterases in vivo leads to liberation of the biologically active androgen, dimethandrolone (DMA), a 19-norandrogen. For hormone replacement in men, administration of C19 androgens such as testosterone (T) may lead to elevations in circulating levels of estrogens due to aromatization. As several reports have suggested that certain 19-norandrogens may serve as substrates for the aromatase enzyme and are converted to the corresponding aromatic A-ring products, it was important to investigate whether DMA, the related compound, 11β-methyl-19-nortestosterone (11β-MNT), also being tested for hormonal therapy in men, and other 19-norandrogens can be converted to aromatic A-ring products by human aromatase. The hypothetical aromatic A-ring product corresponding to each substrate was obtained by chemical synthesis. These estrogens bound with high affinity to purified recombinant human estrogen receptors (ER) α and β in competitive binding assays (IC50's: 5−12 × 10−9 M) and stimulated transcription of 3XERE-luciferase in T47Dco human breast cancer cells with a potency equal to or greater than that of estradiol (E2) (EC50's: 10−12 to 10−11 M). C19 androgens (T, 17α-methyltestosterone (17α-MT), androstenedione (AD), and 16α-hydroxyandrostenedione (16α-OHAD)), 19-norandrogens (DMA, 11β-MNT, 19-nortestosterone (19-NT), and 7α-methyl-19-nortestosterone (MENT)) or the structurally similar 19-norprogestin, norethindrone (NET) were incubated at 50 μM with recombinant human aromatase for 10−180 min at 37 °C. The reactions were terminated by extraction with acetonitrile and centrifugation, and substrate and potential product were separated by HPLC. Retention times were monitored by UV absorption, and UV peaks were quantified using standard curves. Aromatization

Azaborines: Unique Isosteres of Aromatic and Heteroaromatic Systems

NASA Astrophysics Data System (ADS)

Davies, Geraint H. M.

-annulation derivitization of the azaborine cores can allow access to higher order functionalized structures. A method for functionalizing the 2,1-borazaronaphthalene scaffold using ammonium alkylbis(catecholato)silicates via photoredox/nickel dual catalysis was found to be highly effective. By forging Csp3-C sp2 bonds via this approach, alkyl fragments with various functional groups can be introduced to the azaborine core, affording previously inaccessible heterocyclic isosteres in good to excellent yields. These conditions provide sensitive functional group tolerance, even permitting the cross-coupling of unprotected primary and secondary amines. Regioselective C-H borylation and subsequent cross-coupling of the 2,1-borazaronaphthalene core could also be achieved. Although 2,1-borazaronaphthalene is closely related to naphthalene in terms of structure, the argument is made that the former has electronic similarities to indole. Based on that premise, iridium-mediated C-H activation has enabled facile installation of a versatile, nucleophilic coupling handle at a previously inaccessible site of 2,1-borazaronaphthalenes. A variety of substituted 2,1-borazaronaphthalene cores can be successfully borylated and further cross-coupled in a facile manner to yield diverse C(8)-substituted 2,1-borazaronaphthalenes.

Selective treatment to reduce contamination of propolis by polycyclic aromatic hydrocarbons (PAHs) still preserving its active polyphenol component and antioxidant activity.

PubMed

Galeotti, Fabio; Crimaldi, Laura; Maccari, Francesca; Zaccaria, Vincenzo; Fachini, Alfredo; Volpi, Nicola

2017-09-01

The adverse effects on health and environment caused by polycyclic aromatic hydrocarbons (PAHs) are critical problems. EFSA has defined 16 priority PAHs that are both genotoxic and carcinogenic, and identified eight (PAH8) priority PAHs as good indicators of the toxicity and occurrence in food. Food supplements containing propolis were also found to contain relatively high quantities of PAHs. We report about an extractive procedure which is able to purify propolis from a high content of PAHs using a balanced mixture of ethanol and water solvents. Extracts were characterised for total content of polyphenols, for in vitro antioxidant activity, and single classes of polyphenols evaluated by HPLC-ESI-MS. Obtained propolis extracts were found to have PAH8 and specific benzo[a]pyrene content below limits recommended by EFSA. The reported extractive procedure is easily applicable for possible industrial productions and may also be adopted to the purification of polyphenols from other plant extracts and natural sources.

Aromaticity of benzene derivatives: an exploration of the Cambridge Structural Database.

PubMed

Majerz, Irena; Dziembowska, Teresa

2018-04-01

The harmonic oscillator model of aromaticity (HOMA) index, one of the most popular aromaticity indices for solid-state benzene rings in the Cambridge Structural Database (CSD), has been analyzed. The histograms of HOMA for benzene, for benzene derivatives with one formyl, nitro, amino or hydroxy group as well as the histograms for the derivatives with two formyl, nitro, amino or hydroxy groups in ortho, meta and para positions were investigated. The majority of the substituted benzene derivatives in the CSD are characterized by a high value of HOMA, indicating fully aromatic character; however, the distribution of the HOMA value from 1 to about 0 indicates decreasing aromaticity down to non-aromatic character. Among the benzene derivatives investigated, a significant decrease in aromaticity can be related to compounds with diamino and dinitro groups in the meta position.

All the catalytic active sites of MoS 2 for hydrogen evolution

DOE PAGES

Li, Guoqing; Zhang, Du; Qiao, Qiao; ...

2016-11-29

MoS 2 presents a promising low-cost catalyst for the hydrogen evolution reaction (HER), but the understanding about its active sites has remained limited. Here we present an unambiguous study of the catalytic activities of all possible reaction sites of MoS 2, including edge sites, sulfur vacancies, and grain boundaries. We demonstrate that, in addition to the well-known catalytically active edge sites, sulfur vacancies provide another major active site for the HER, while the catalytic activity of grain boundaries is much weaker. Here, the intrinsic turnover frequencies (Tafel slopes) of the edge sites, sulfur vacancies, and grain boundaries are estimated tomore » be 7.5 s –1 (65–75 mV/dec), 3.2 s –1 (65–85 mV/dec), and 0.1 s –1 (120–160 mV/dec), respectively. We also demonstrate that the catalytic activity of sulfur vacancies strongly depends on the density of the vacancies and the local crystalline structure in proximity to the vacancies. Unlike edge sites, whose catalytic activity linearly depends on the length, sulfur vacancies show optimal catalytic activities when the vacancy density is in the range of 7–10%, and the number of sulfur vacancies in high crystalline quality MoS 2 is higher than that in low crystalline quality MoS 2, which may be related with the proximity of different local crystalline structures to the vacancies.« less

Anaerobic Catabolism of Aromatic Compounds: a Genetic and Genomic View

PubMed Central

Carmona, Manuel; Zamarro, María Teresa; Blázquez, Blas; Durante-Rodríguez, Gonzalo; Juárez, Javier F.; Valderrama, J. Andrés; Barragán, María J. L.; García, José Luis; Díaz, Eduardo

2009-01-01

Summary: Aromatic compounds belong to one of the most widely distributed classes of organic compounds in nature, and a significant number of xenobiotics belong to this family of compounds. Since many habitats containing large amounts of aromatic compounds are often anoxic, the anaerobic catabolism of aromatic compounds by microorganisms becomes crucial in biogeochemical cycles and in the sustainable development of the biosphere. The mineralization of aromatic compounds by facultative or obligate anaerobic bacteria can be coupled to anaerobic respiration with a variety of electron acceptors as well as to fermentation and anoxygenic photosynthesis. Since the redox potential of the electron-accepting system dictates the degradative strategy, there is wide biochemical diversity among anaerobic aromatic degraders. However, the genetic determinants of all these processes and the mechanisms involved in their regulation are much less studied. This review focuses on the recent findings that standard molecular biology approaches together with new high-throughput technologies (e.g., genome sequencing, transcriptomics, proteomics, and metagenomics) have provided regarding the genetics, regulation, ecophysiology, and evolution of anaerobic aromatic degradation pathways. These studies revealed that the anaerobic catabolism of aromatic compounds is more diverse and widespread than previously thought, and the complex metabolic and stress programs associated with the use of aromatic compounds under anaerobic conditions are starting to be unraveled. Anaerobic biotransformation processes based on unprecedented enzymes and pathways with novel metabolic capabilities, as well as the design of novel regulatory circuits and catabolic networks of great biotechnological potential in synthetic biology, are now feasible to approach. PMID:19258534

Development of genetically engineered bacteria for production of selected aromatic compounds

DOEpatents

Ward, Thomas E.; Watkins, Carolyn S.; Bulmer, Deborah K.; Johnson, Bruce F.; Amaratunga, Mohan

2001-01-01

The cloning and expression of genes in the common aromatic pathway of E. coli are described. A compound for which chorismate, the final product of the common aromatic pathway, is an anabolic intermediate can be produced by cloning and expressing selected genes of the common aromatic pathway and the genes coding for enzymes necessary to convert chorismate to the selected compound. Plasmids carrying selected genes of the common aromatic pathway are also described.

Machine-Learning Methods Enable Exhaustive Searches for Active Bimetallic Facets and Reveal Active Site Motifs for CO 2 Reduction

DOE PAGES

Ulissi, Zachary W.; Tang, Michael T.; Xiao, Jianping; ...

2017-07-27

Bimetallic catalysts are promising for the most difficult thermal and electrochemical reactions, but modeling the many diverse active sites on polycrystalline samples is an open challenge. Here, we present a general framework for addressing this complexity in a systematic and predictive fashion. Active sites for every stable low-index facet of a bimetallic crystal are enumerated and cataloged, yielding hundreds of possible active sites. The activity of these sites is explored in parallel using a neural-network-based surrogate model to share information between the many density functional theory (DFT) relaxations, resulting in activity estimates with an order of magnitude fewer explicit DFTmore » calculations. Sites with interesting activity were found and provide targets for follow-up calculations. This process was applied to the electrochemical reduction of CO 2 on nickel gallium bimetallics and indicated that most facets had similar activity to Ni surfaces, but a few exposed Ni sites with a very favorable on-top CO configuration. This motif emerged naturally from the predictive modeling and represents a class of intermetallic CO 2 reduction catalysts. These sites rationalize recent experimental reports of nickel gallium activity and why previous materials screens missed this exciting material. Most importantly these methods suggest that bimetallic catalysts will be discovered by studying facet reactivity and diversity of active sites more systematically.« less

Machine-Learning Methods Enable Exhaustive Searches for Active Bimetallic Facets and Reveal Active Site Motifs for CO 2 Reduction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ulissi, Zachary W.; Tang, Michael T.; Xiao, Jianping

Bimetallic catalysts are promising for the most difficult thermal and electrochemical reactions, but modeling the many diverse active sites on polycrystalline samples is an open challenge. Here, we present a general framework for addressing this complexity in a systematic and predictive fashion. Active sites for every stable low-index facet of a bimetallic crystal are enumerated and cataloged, yielding hundreds of possible active sites. The activity of these sites is explored in parallel using a neural-network-based surrogate model to share information between the many density functional theory (DFT) relaxations, resulting in activity estimates with an order of magnitude fewer explicit DFTmore » calculations. Sites with interesting activity were found and provide targets for follow-up calculations. This process was applied to the electrochemical reduction of CO 2 on nickel gallium bimetallics and indicated that most facets had similar activity to Ni surfaces, but a few exposed Ni sites with a very favorable on-top CO configuration. This motif emerged naturally from the predictive modeling and represents a class of intermetallic CO 2 reduction catalysts. These sites rationalize recent experimental reports of nickel gallium activity and why previous materials screens missed this exciting material. Most importantly these methods suggest that bimetallic catalysts will be discovered by studying facet reactivity and diversity of active sites more systematically.« less

Mutation at a strictly conserved, active site tyrosine in the copper amine oxidase leads to uncontrolled oxygenase activity.

PubMed

Chen, Zhi-Wei; Datta, Saumen; Dubois, Jennifer L; Klinman, Judith P; Mathews, F Scott

2010-08-31

The copper amine oxidases carry out two copper-dependent processes: production of their own redox-active cofactor (2,4,5-trihydroxyphenylalanine quinone, TPQ) and the subsequent oxidative deamination of substrate amines. Because the same active site pocket must facilitate both reactions, individual active site residues may serve multiple roles. We have examined the roles of a strictly conserved active site tyrosine Y305 in the copper amine oxidase from Hansenula polymorpha kinetically, spetroscopically (Dubois and Klinman (2006) Biochemistry 45, 3178), and, in the present work, structurally. While the Y305A enzyme is almost identical to the wild type, a novel, highly oxygenated species replaces TPQ in the Y305F active sites. This new structure not only provides the first direct detection of peroxy intermediates in cofactor biogenesis but also indicates the critical control of oxidation chemistry that can be conferred by a single active site residue.

Aromatic Amino Acids and Related Substances: Chemistry, Biology, Medicine, and Application

USDA-ARS?s Scientific Manuscript database

On the occasion of the "Transdisciplinary International Conference on Aromatic Amino Acids and Related Substances," the organizing committee honors and thanks the expert participants from many areas of aromatic amino acid (AAA)3 research. In this transdisciplinary meeting, "aromatic paradigms" were ...

Aromatic ring generation as a dust precursor in acetylene discharges

NASA Astrophysics Data System (ADS)

De Bleecker, Kathleen; Bogaerts, Annemie; Goedheer, Wim

2006-04-01

Production of aromatic hydrocarbon compounds as an intermediate step for particle formation in low-pressure acetylene discharges is investigated via a kinetic approach. The detailed chemical reaction mechanism contains 140 reactions among 55 species. The cyclic hydrocarbon chemistry is mainly based on studies of polycyclic aromatic hydrocarbon formation in cosmic environments. The model explicitly includes organic chain, cyclic molecules, radicals, and ions up to a size of 12 carbon atoms. The calculated density profiles show that the aromatic formation yields are quite significant, suggesting that aromatic compounds play a role in the underlying mechanisms of particle formation in hydrocarbon plasmas.

Does the concept of Clar's aromatic sextet work for dicationic forms of polycyclic aromatic hydrocarbons?--testing the model against charged systems in singlet and triplet states.