The inner filter effects and their correction in fluorescence spectra of salt marsh humic matter

The inner filter effects in synchronous fluorescence spectra (Δλ = 60 nm) of sedimentary humic substances from a salt marsh were studied. Accordingly to their type and the influence of plant colonization, these humic substances have different spectral features and the inner filter effects act in a different manner. The fluorescence spectra of the humic substances from sediments with colonizing plants have a protein like band (λ_exc = 280 nm) which is strongly affected by primary and secondary inner filter effects. These effects were also observed for the bands situated at longer wavelengths, i.e., at λ_exc = 350 nm and λ_ex = 454 nm for the fulvic acids (FA) and humic acids (HA), respectively. However, they are more important for the band at 280 nm, causing spectral distortions which can be clearly seen when the spectra of solutions 40 mg L⁻¹ of different samples (Dissolved Organic Carbon – DOC ∼ 20 mg L⁻¹) are compared with and without correction of the inner filter effects. The importance of the spectral distortions caused by inner filter effects has been demonstrated in solutions containing a mixture of model compounds which represent the fluorophores detected in the spectra of sedimentary humic samples. The effectiveness of the mathematical correction of the inner filter effects in the spectra of those solutions and of solutions of sedimentary humic substances was studied. It was observed that inner filter effects in the sedimentary humic substances spectra can be mathematically corrected, allowing to obtain a linear relationship between the fluorescence intensity and humic substances concentration and preventing distortions at concentrations as high as 50 mg L⁻¹ which otherwise would obscure the protein like band.     

Quantitative Series Enrichment Analysis (QSEA): a novel procedure for 3D-QSAR analysis

A novel procedure is proposed for 3D-QSAR analysis. The composition of 16 published QSAR datasets has been examined using Quantitative Series Enrichment Analysis (QSEA). The procedure is based on topomer technologies. A heatmap display in combination with topomer CoMFA and a novel series trajectory analysis revealed critical information for the assembly of structures into meaningful series. Global and local centroid structures can be determined from a similarity distance matrix and build the origins for stepwise model building by increasing the similarity radius around the centroid nucleus. The results indicate that the new procedure allows determination of whether compounds belong to an emerging structure-activity relationship and which compounds can be predicted within reliable limits.     

Rotational line-integrated photoabsorption cross sections corresponding to the delta(0,0) band of NO: a molecular quantum-defect orbital procedure

The rotational line-integrated photoabsorption cross sections corresponding to the delta(0,0) band of the nitric oxide (NO) molecule at 295 K, calculated with the molecular quantum-defect orbital methodology, are in rather good accord with the experimental measurements available in the literature. The achieved results are of straightforward use in atmospheric chemistry, such as in the assessment of the NO photodissociation rate constant, which is of great relevance for atmospheric modeling.     

Monitoring and effects of nicosulfuron in aquatic mesocosms: development of a simple analytical procedure and evidence for low toxicity to phytoplankton communities

A new analytical procedure is proposed for monitoring nicosulfuron (sulfonylurea herbicide) in aquatic mesocosms derived from complex ecosystems. The approach is based on alternate use of the anionic and molecular forms of the pesticide during the procedure. It also takes into account the sensitivity of the molecule to hydrolysis. The procedure involves solid-phase extraction on a polystyrene–divinylbenzene support followed by a conventional high-performance liquid chromatographic analysis with UV-diode array detection. Recovery tests on samples from natural waters demonstrated that the performances obtained were convenient for monitoring aquatic mesocosms (recoveries of 91±12% at 0.5 g L^–1). The method was used to monitor nicosulfuron in mesocosms initially spiked at 2 or 30 g L^–1 . The evolution curves were compared to those obtained from mesocosms contaminated with atrazine at the same initial doses. The sensitivity of phytoplankton communities to nicosulfuron in aquatic mesocosms was found to be very limited.     

Thermal and structural changes of photosynthetic reaction centers characterized by photoacoustic detection with a broad frequency band hydrophone.

Photoacoustic measurements using a broad frequency band hydrophone were carried out in photosynthetic reaction centers (RC) isolated from Rhodobacter sphaeroides R-26 purple bacteria. Data were extracted on enthalpy and volume changes accompanying the primary steps after excitation in the range of 0-500 microseconds aimed at further characterizing the thermodynamic properties of the RC. Quinone titration showed that the volume contraction accompanying the electron transport is sensitive to the molecular species occupying the secondary quinone site. delta VM = 14.4, 7.7 and 4.3 cm3 molar volume contractions were calculated from the measured parameters for 1, 2 and 0.07 quinone/RC after light excitation. Comparing the enthalpy changes (delta H) to the Gibbs free energy data in the literature, a rather large (26%) entropic contribution to the free energy changes (delta G) is estimated for the P*QAQB-->P+QA-QB electron transport (where QA and QB represent primary and secondary quinones, respectively). This is in contrast to previous estimations that delta G = delta H in these processes. On the other hand, only a small (4%) entropic contribution to the delta G of the P*QAQB-->P+QAQB- process is estimated, in agreement with the literature data. Our results are in good agreement with the data obtained earlier (Edens et al. [2000] J. Am. Chem. Soc. 122, 1479-1485).     

Flexible enzymatic and chemo-enzymatic approaches to a broad range of uridine-diphospho-sugars

Enzymatic and chemo-enzymatic approaches provide straightforward access to uridine diphospho sugars irrespective of the relative and absolute configuration of the sugar, its ring size and substitution pattern.     

Molecular shape diversity of combinatorial libraries: a prerequisite for broad bioactivity

A computational method to rapidly assess and visualize the diversity in molecular shape associated with a given compound set has been developed. Normalized ratios of principal moments of inertia are plotted into two-dimensional triangular graphs and then used to compare the shape space covered by different compound sets, such as combinatorial libraries of varying size and composition. We have further developed a computational method to analyze interset similarity in terms of shape space coverage, which allows the shape redundancy between the different subsets of a given compound collection to be analyzed in a quantitative way. The shape space coverage has been found to originate mainly from the nature and the 3D-geometry (but not the size) of the central scaffold, while the number and nature of the peripheral substituents and conformational aspects were shown to be of minor importance. Substantial shape space coverage has been correlated with broad biological activity by applying the same shape analysis to collections of known bioactive compounds, such as MDDR and the GOLD-set. The aggregate of our results corroborates the intuitive notion that molecular shape is intimately linked to biological activity and that a high degree of shape (hence scaffold) diversity in screening collections will increase the odds of addressing a broad range of biological targets.     

Quantitative trace analysis of a broad range of antiviral drugs in poultry muscle using column-switch liquid chromatography coupled to tandem mass spectrometry

A liquid chromatography–tandem mass spectrometry method for the analysis of seven antiviral drugs, zanamivir, ribavirin, oseltamivir, oseltamivir carboxylate, amantadine, rimantadine and arbidol, in poultry muscle is reported. The antiviral drugs were extracted from the homogenized poultry muscle sample using methanol. The extract was purified using tandem solid-phase extraction combining a cation exchange cartridge and a phenylboronic acid cartridge. To prevent excessive matrix effects, the analytes were separated from the matrix constituents using a column-switch liquid chromatography system combining a reversed-phase and a Hypercarb analytical column. Detection was carried out using tandem mass spectrometry. The method was fully validated according to 2002/657/EC [1] and proved to be adequate for quantification and confirmation of zanamivir and ribavirin at 10 μg kg⁻¹, oseltamivir, oseltamivir carboxylate, amantadine and rimantadine at levels below 1.0 μg kg⁻¹ and for qualitative confirmatory analysis of arbidol at levels below 1 μg kg⁻¹.     

Communication: Clusters of absorbing disks on a reflecting wall: competition for diffusing particles

Trapping of diffusing particles by a cluster of absorbing disks on the otherwise reflecting wall is a manifestly many-body problem because of the disk competition for the particles. By replacing the cluster with an effective uniformly absorbing spot, we derive a simple formula for the rate constant that characterizes the trapping. The formula shows how the rate constant depends on the size and shape of the cluster.     

The correct and incorrect way to calibrate a Compton suppression counting system for gamma-ray efficiency

Gamma-ray efficiency calculations for a germanium detector have been made for a Compton suppression system. Results have shown that for radionuclides that have gamma rays in coincidence the photopeaks can be severely depressed leading to erroneous results. While this can be overcome in routine neutron activation analysis using a comparator method, special consideration must be given to determine the suppression for coincident gamma rays when calculating the efficiency curve and for radionuclide activities. This is especially important for users of the k ₀ method and for fission product identification using Compton suppression methods.     

Fluorometric determination and imaging of glutathione based on a thiol-triggered inner filter effect on the fluorescence of carbon dots

The authors describe a sensitive method for determination of glutathione (GSH) that is based on a thiol-triggered inner filter effect on the fluorescence of N-doped carbon dots (N-doped CDs). N-doped CDs with a quantum yield as high as 31% were prepared by a one-pot procedure, and 5,5′-dithiobis-(2-nitrobenzoic acid) was employed as a reagent for GSH recognition. The reaction product (5-thio-2-nitrobenzoic acid; TNB) acts as an absorber of the 410-nm light used to photo-excite the N-doped CDs. Hence, the fluorescence of N-doped CDs (peaking at 510 nm) is reduced with increasing concentrations of GSH. As little as 30 nM of GSH can be detected by this method. The approach was successfully applied to (a) food analysis, (b) an investigation of an oxidative stress model, and (c) to live cells imaging. The method does not require the surface of N-doped CDs to be chemically modified, and a linkage between receptor and fluorophore is not needed. In our perception, the method may become a viable tool for the detection and imaging of thiols.

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Graphical abstract Fluorescence sensing strategy for glutathione detection based on a thiol-triggered inner filter effect via new N-doped carbon dots and application to food analysis, oxidative stress study and cell imaging.

     

From a rock to a hard place: Journeys of a radiochemist through inner and outer space

A brief chronicle is presented of one radiochemist's meanders through the fields of meteoritics, lunar studies, and geochemistry to current studies of possible relationships of trace element imbalances to diseases affecting the brain and spinal cord. This range of studies is used to underscore the broad applications of radiochemistry and the need to maintain educational programs and research in radiochemistry. Our recent studies of tissues from subjects with Alzheimer's disease (AD) and amyotrophic lateral sclerosis (ALS), have shown that imbalances exist for concentrations of many trace elements, compared to corresponding concentrations in control subjects. Among the elements most frequently found imbalanced are aluminum, bromine, cadmium, copper, iron, mercury, rubidium, and zinc. Several of these elements may be involved in processes leading to free-radical-induced oxidative damage in Alzheimer's disease. Our multi-technique analytical approach to these studies is briefly reviewed.     

Networking of calixcrowns: from heteronuclear endo/exocyclic coordination polymers to a photoluminescence switch

Solvato-PL switching and shrinking-and-opening process: we present two CuI coordination polymers of calix[4]-bis-monothiacrown (L) obtained in the absence (1) and presence (2) of KI. The structures show not only very unusual CuI-based network arrangements but also unique reversible photolunimescence switching behavior induced by removal of coordinated solvent. Furthermore, upon inclusion of K+ ions the crown ring shrinks leading to "opening" of opposite aromatic rings in the host calixarene unit, rare behavior for this class of compound.     

Coarse-graining: a procedure to generate equilibrated and relaxed models of amorphous polymers

We present a coarse-graining procedure to construct models of amorphous polymers. The method, which was applied to polyethylene, is based on a generation-relaxation strategy previously developed to provide independent atomistic microstructures. The coarse-graining was performed by assigning positions to mesoscopic particles denoted blobs, which represent groups of atoms, through distance, angle and dihedral distribution functions. The interaction energy between pairs of blobs was evaluated through a soft potential, whose parameters were derived from atomistic models. Three levels of coarse-graining that differ in the number of atoms included in the blob have been considered. The structural and energy-related properties calculated using the coarse-grained models developed in this study are in good agreement with those obtained using atomistic simulations.     

New implementation of a program to calculate correlated band structures of polymers: An application to the band structure of polyparaphenylene (PPP)

A new program has recently been implemented with the aim of extending quasi-particle (QP) band structure calculations to polymers with larger unit cells. The theoretical background is briefly reviewed and the new algorithm described, which has been optimized for machines with vector processors. To illustrate the usefulness of this technique, calculations have been performed on polyparaphenylene (PPP) using a double-zeta basis set. The calculated QP band gap between the valence and conduction bands is 2.3 eV, which compares favorably with the experimental value of 2.8 eV. The self-consistent field (SCF) result with the same double-zeta basis set is 8.7 eV. © 1994 by John Wiley & Sons, Inc.     

Mapping atomistic simulations to mesoscopic models: a systematic coarse-graining procedure for vinyl polymer chains

The paper introduces a systematic procedure to coarse-grain atomistic models of the largest family of synthetic polymers into a mesoscopic model that is able to keep detailed information about chain stereosequences. The mesoscopic model consists of sequences of superatoms centered on methylene carbons of two different types according to the kind of diad (m or r) they belong to. The corresponding force-field contains three different bonds, six angle and three nonbonded terms. Recently developed analytical potentials, based on sums of Gaussians for bond and angle terms of the mesoscale force field have been used. For the nonbonded part, numerical potentials optimized by pressure-corrected iterative Boltzmann inversion have been used. As test case we coarse-grained an atomistic all-atom model of atactic polystyrene. The proposed mesoscale model has been successfully tested against structural and dynamical properties for different chain lengths and opens the possibility of relaxing melts of high molecular weight vinyl polymers.     

From mesoscale back to atomistic models: a fast reverse-mapping procedure for vinyl polymer chains

This paper introduces a systematic procedure to obtain well-relaxed atomistic melt structures from mesocale models of vinyl polymers based on sequences of diads. Following the methodology introduced by Milano and Müller-Plathe [J. Phys. Chem. B. 2005, 109, 18609], coarse-grain models consisting of sequences of superatoms of two different types meso and racemo have been used to relax mesocale melts of atactic and syndiotactic polystyrene. The proposed method, based on a fully geometrical approach, does not involve expensive potential energy and force evaluations and allows a very fast and efficient reconstruction of the atomistic detail. The method, successfully tested against experimental data, allows us to obtain all atom models of both stereoregular and stereoirregular polymers and opens the possibility of relaxing large molecular weight melts of vinyl chains.     

Cd(II) and Cu(II) coordination polymers based on a multidentate N-donor ligand: syntheses,crystal structures,optical band gaps,and photoluminescence

Four Cd(II)- and Cu(II)-containing coordination polymers (CPs) based on a multidentate N-donor ligand and varied dicarboxylate anions, [Cd(3,3′-tmbpt)(p-bdc)]·2.5H₂O (1), [Cd(3,3′-tmbpt)(m-bdc)]·2H₂O (2), [Cu(3,3′-tmbpt)(m-bdc)]·H₂O (3), and [Cu(3,3′-tmbpt)(p-bdc)]·2H₂O (4), where 3,3′-tmbpt = 1 ? ((1H-1,2,4-triazol-1-yl)methyl)-3,5-bis(3-pyridyl)-1,2,4-triazole, p-H₂bdc = 1,4-benzenedicarboxylic acid, and m-H₂bdc = 1,3-benzenedicarboxylic acid, have been prepared hydrothermally. The structures of the compounds were determined by single-crystal X-ray diffraction analyses and further characterized by infrared spectra and elemental analyses. Compound 1 exhibits a 3-D twofold interpenetrating framework with a 6⁵·8 CdSO₄ topology. Compound 2 is a 2-D layer containing meso-helical chains with a 4⁴·6² sql topology. Compound 3 shows a 1-D → 3-D interdigitated architecture while 4 displays a 2-D → 3-D interdigitated architecture. The structural differences of the compounds indicate that the dicarboxylate anions and the central metal ions play important roles in the resulting structures of CPs. Optical band gaps and solid-state photoluminescent properties have also been studied.     

Application of a microfluidic reaction system for CdSe nanocrystal preparation: their growth kinetics and photoluminescence analysis

We used a microreactor for CdSe nanocrystal preparation and explored the effects of experimental conditions on the properties of the products. The particle growth kinetics and photoluminescence properties of the nanocrystals showed identical trends to previous reports, indicating the efficiency of the current method for analysis of rapid nanocrystal synthesis as well as industrial production of CdSe nanocrystals.     

Aptasensor for visual and fluorometric determination of lysozyme based on the inner filter effect of gold nanoparticles on CdTe quantum dots

The authors describe an aptasensor for visual and fluorescent detection of lysozyme via an inner filter effect (IFE). The assay is based on the fact that red gold nanoparticles (AuNPs) act as powerful absorbers of the green fluorescence of CdTe because of spectral overlap. If the lysozyme-binding aptamer is adsorbed onto the surface of the AuNPs, the salt-induced aggregation of AuNPs (that leads to a color change from red to blue) does not occur and the IFE remains efficient. If lysozyme is present, it will bind the aptamer and thereby prevent its adsorption on the AuNPs. As a result, the salt-triggered aggregation of the AuNPs will occur. Consequently, color will change from red to blue, and green fluorescence will pop up because the IFE is suppressed. Under optimum conditions, fluorescence is linearly related to lysozyme concentration in the 1.0 nM to 20 nM concentration range, with a 0.55 nM limit of detection. The method is perceived to be of wider applicability in that it may be used to design other visual and fluorescent assays if appropriate aptamers are available.

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Graphical abstract The fluorescence intensity of QDs is quenched by gold nanoparticles (AuNPs) due to an inner filter effect. Aptamers can adsorb on AuNPs to prevent the salt-induced aggregation. AuNPs serve a dual function as fluorescence quencher and colorimetric reporter.