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  • 1
    Language: English
    In: Chemosphere, April 2017, Vol.172, pp.175-184
    Description: Fluorescence and UV/Vis spectra of aqueous solutions with numerous organic compounds are a superposition of single spectra of the chemical species present. Thus, an isolation of individual spectra with chemometrics is required for their quantification. We investigated UV/Vis spectra and fluorescence excitation-emission matrices of vanillic acid, salicylic acid, phenoxyacetic acid and phthalic acid with positive matrix factorization (PMF) and non-negativity constrained parallel factor analysis (PARAFAC) in combination with the law of mass action. In consideration of the pH-dependent speciation of organic acids, we first reconstructed the pH-specific spectra of each compound. Using these spectra as known components in a constrained algorithm, we could successfully quantify species of multiple compounds and reconstruct the solution pH. In addition, we estimated the uncertainty of reconstructed spectra and concentrations in order to assess the most probable number of components for PMF/PARAFAC. Therefore, we could derive a framework to reconstruct the number of relevant species and their individual concentration present in spectroscopic data of aqueous solutions containing multiple organic compounds.
    Keywords: Parallel Factor Analysis (Parafac) ; Positive Matrix Factorization (Pmf) ; Organic Acid ; Environmental Tracer ; Number of Components ; Chemistry ; Ecology
    ISSN: 0045-6535
    E-ISSN: 1879-1298
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  • 2
    Language: English
    In: Geochimica et Cosmochimica Acta, 15 November 2015, Vol.169, pp.167-183
    Description: Iron oxides represent a substantial fraction of secondary minerals and particularly affect the reactive properties of natural systems in which they formed, e.g. in soils and sediments. Yet, it is still obscure how transient conditions in the solution will affect the properties of in situ precipitated Fe oxides. Transient compositions, i.e. compositions that change with time, arise due to predominant non-equilibrium states in natural systems, e.g. between liquid and solid phases in soils. In this study, we characterize Fe–OM co-precipitates that formed in pH-neutral exfiltrates from anoxic topsoils under transient conditions. We applied soil column outflow experiments, in which Fe was discharged with the effluent from anoxic soil and subsequently oxidized in the effluent due to contact with air. Our study features three novel aspects being unconsidered so far: (i) the transient composition of soil-derived solutions, (ii) that pedogenic Fe oxides instead of Fe salts serve as major source for Fe in soil solution and (iii) the presence of exclusively soil-derived organic and inorganic compounds during precipitation. The experiments were carried out with two topsoil materials that differed in composition, texture and land use. Derived from Mössbauer spectroscopy, broad distributions in quadrupole splittings (0–2 mm s ) and magnetic hyperfine fields (35–53 T) indicated the presence of low-crystalline ferrihydrite and even lower crystalline Fe phases in all Fe–OM co-precipitates. There was no unequivocal evidence for other Fe oxides, i.e. lepidocrocite and (nano)goethite. The Fe–OM co-precipitates contained inorganic (P, sulfate, silicate, Al, As) and organic compounds (proteins, polysaccharides), which were concurrently discharged from the soils. Their content in the Fe–OM co-precipitates was controlled by their respective concentration in the soil-derived solution. On a molar basis, OC and Fe were the main components in the Fe–OM co-precipitates (OC/Fe ratio = 0.5–2). The elemental composition of the Fe–OM co-precipitates was in accordance with the sequential precipitation of Fe(III)phosphates/arsenates prior to the formation of ferrihydrite. This explains decreasing Si contents in the Fe–OM co-precipitates with increasing availability of P. With respect to constant mean quadrupole splittings and slightly decreasing mean magnetic hyperfine fields, increasing contents of OC, P and Al in the Fe–OM co-precipitates did not further increase the structural disorder of the Fe polyhedra, while the crystallite interactions slightly decreased. Scanning electron microscopy and dynamic light scattering revealed the coincidental presence of variably sized aggregates and a considerable amount of Fe–OM co-precipitates, which remained dispersed in solution for months. Thus, variably composed Fe–OM co-precipitates with highly diverse aggregate sizes and comparably constant poor crystallinity can be expected after the oxidation of Fe in transient, soil-derived solutions.
    Keywords: Geology
    ISSN: 0016-7037
    E-ISSN: 1872-9533
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  • 3
    Language: English
    In: The Journal of Physical Chemistry C, 10/09/2014, Vol.118(40), pp.23349-23360
    ISSN: 1932-7447
    E-ISSN: 1932-7455
    Source: American Chemical Society (via CrossRef)
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  • 4
    Language: English
    In: Analytical and Bioanalytical Chemistry, 2011, Vol.399(3), pp.1215-1222
    Description: Novel fluorescent nanosensors, based on a naphthyridine receptor, have been developed for the detection of guanosine nucleotides, and both their sensitivity and selectivity to various nucleotides were evaluated. The nanosensors were constructed from polystyrene nanoparticles functionalized by ( N -(7-((3-aminophenyl)ethynyl)-1,8-naphthyridin-2-yl)acetamide) via carbodiimide ester activation. We show that this naphthyridine nanosensor binds guanosine nucleotides preferentially over adenine, cytosine, and thymidine nucleotides. Upon interaction with nucleotides, the fluorescence of the nanosensor is gradually quenched yielding Stern–Volmer constants in the range of 2.1 to 35.9 mM −1 . For all the studied quenchers, limits of detection (LOD) and tolerance levels for the nanosensors were also determined. The lowest (3σ) LOD was found for guanosine 3’,5’-cyclic monophosphate (cGMP) and it was as low as 150 ng/ml. In addition, we demonstrated that the spatial arrangement of bound analytes on the nanosensors’ surfaces is what is responsible for their selectivity to different guanosine nucleotides. We found a correlation between the changes of the fluorescence signal and the number of phosphate groups of a nucleotide. Results of molecular modeling and ζ-potential measurements confirm that the arrangement of analytes on the surface provides for the selectivity of the nanosensors. These fluorescent nanosensors have the potential to be applied in multi-analyte, array-based detection platforms, as well as in multiplexed microfluidic systems. Figure Naphthyridine_receptor
    Keywords: Naphthyridine receptor ; cGMP ; Base pairing ; Nucleotide nanosensor ; Fluorescence spectroscopy
    ISSN: 1618-2642
    E-ISSN: 1618-2650
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  • 5
    Language: English
    In: The Journal of Chemical Thermodynamics, July, 2013, Vol.62, p.211(11)
    Description: To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.jct.2013.03.011 Byline: Neha Awasthi, Thomas Ritschel, Reinhard Lipowsky, Volker Knecht Abstract: acents [DELTA]G and K.sup.eq for NO.sub.2 dimerization and NH.sub.3 synthesis calculated via ab-initio methods. acents Vis-a-vis experiments, W1 and CCSD(T) are accurate and G3B3 also does quite well. acents CBS-APNO most accurate for NH.sub.3 reaction but shows limitations in modeling NO.sub.2. acents Temperature dependence of [DELTA]G and K.sup.eq is calculated for the NH.sub.3 reaction. acents Good agreement of calculated K.sup.eq with experiments and the van't Hoff approximation. Article History: Received 4 January 2013; Revised 11 March 2013; Accepted 15 March 2013
    ISSN: 0021-9614
    Source: Cengage Learning, Inc.
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  • 6
    In: Water Resources Research, March 2016, Vol.52(3), pp.2206-2221
    Description: Transport studies that employ column experiments in closed‐flow mode complement classical approaches by providing new characteristic features observed in the solute breakthrough and equilibrium between liquid and solid phase. Specific to the closed‐flow mode is the recirculation of the effluent to the inflow via a mixing vessel. Depending on the ratio of volumes of mixing vessel and water‐filled pore space, a damped oscillating solute concentration emerges in the effluent and mixing vessel. The oscillation characteristics, e.g., frequency, amplitude, and damping, allow for the investigation of solute transport in a similar fashion as known for classical open‐flow column experiments. However, the closed loop conserves substances released during transport within the system. In this way, solute and porous medium can equilibrate with respect to physicochemical conditions. With this paper, the features emerging in the breakthrough curves of saturated column experiments run in closed‐flow mode and methods of evaluation are illustrated under experimental boundary conditions forcing the appearance of oscillations. We demonstrate that the effective pore water volume and the pumping rate can be determined from a conservative tracer breakthrough curve uniquely. In this way, external preconditioning of the material, e.g., drying, can be avoided. A reactive breakthrough experiment revealed a significant increase in the pore water pH value as a consequence of the closed loop. These results highlight the specific impact of the closed mass balance. Furthermore, the basis for the modeling of closed‐flow experiments is given by the derivation of constitutive equations and numerical implementation, validated with the presented experiments. A complementary approach of conducting column experiments is presented Concentration oscillations emerge in closed‐flow column experiments A numerical model was developed and successfully applied to observations
    Keywords: Miscible Displacement ; Parameter Identification ; Inverse Modeling ; Equilibrium ; Retardation
    ISSN: 0043-1397
    E-ISSN: 1944-7973
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  • 7
    In: Water Resources Research, August 2016, Vol.52(8), pp.6094-6110
    Description: The identification of transport parameters by inverse modeling often suffers from equifinality or parameter correlation when models are fitted to measurements of the solute breakthrough in column outflow experiments. This parameter uncertainty can be approached by performing multiple experiments with different sets of boundary conditions, each provoking observations that are uniquely attributable to the respective transport processes. A promising approach to further increase the information potential of the experimental outcome is the closed‐flow column design. It is characterized by the recirculation of the column effluent into the solution supply vessel that feeds the inflow, which results in a damped sinusoidal oscillation in the breakthrough curve. In order to reveal the potential application of closed‐flow experiments, we present a comprehensive sensitivity analysis using common models for adsorption and degradation. We show that the sensitivity of inverse parameter determination with respect to the apparent dispersion can be controlled by the experimenter. For optimal settings, a decrease in parameter uncertainty as compared to classical experiments by an order of magnitude is achieved. In addition, we show a reduced equifinality between rate‐limited interactions and apparent dispersion. Furthermore, we illustrate the expected breakthrough curve for equilibrium and nonequilibrium adsorption, the latter showing strong similarities to the behavior found for completely mixed batch reactor experiments. Finally, breakthrough data from a reactive tracer experiment is evaluated using the proposed framework with excellent agreement of model and experimental results. Dispersion is fitted with a tenfold decrease in uncertainty in closed‐flow experiments Equifinality between adsorption kinetics and dispersion is decreased Closed‐flow mode breakthrough curves resemble equilibration curves of completely mixed batch reactor experiments
    Keywords: Miscible Displacement ; Equifinality ; Dispersion ; Kinetics ; Rate Limitation ; Inverse Modeling
    ISSN: 0043-1397
    E-ISSN: 1944-7973
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  • 8
    Language: English
    In: The Journal of Chemical Thermodynamics, July 2013, Vol.62, pp.211-221
    Description: Standard quantum chemical methods are used for accurate calculation of thermochemical properties such as enthalpies of formation, entropies and Gibbs energies of formation. Equilibrium reactions are widely investigated and experimental measurements often lead to a range of reaction Gibbs energies and equilibrium constants. It is useful to calculate these equilibrium properties from quantum chemical methods in order to address the experimental differences. Furthermore, most standard calculation methods differ in accuracy and feasibility of the system size. Hence, a systematic comparison of equilibrium properties calculated with different numerical algorithms would provide a useful reference. We select two well-known gas phase equilibrium reactions with small molecules: covalent dimer formation of NO (2NO N O ) and the synthesis of NH (N + 3 H 2NH ). We test four quantum chemical methods denoted by G3B3, CBS-APNO, W1 and CCSD(T) with aug-cc-pVXZ basis sets (X = 2, 3, and 4), to obtain thermochemical data for NO , N O , and NH . The calculated standard formation Gibbs energies are used to calculate standard reaction Gibbs energies and standard equilibrium constants for the two reactions. Standard formation enthalpies are calculated in a more reliable way using high-level methods such as W1 and CCSD(T). Standard entropies for the molecules are calculated well within the range of experiments for all methods, however, the values of standard formation Gibbs energies show some dependence on the choice of the method. High-level methods perform better for the calculation of molecular energies, however, simpler methods such as G3B3 and CBS-APNO perform quite well in the calculation of total reaction energies and equilibrium constants, provided that the chemical species involved do not exhibit molecular geometries that are difficult to handle by the applied method. The temperature dependence of standard reaction Gibbs energy for the NH reaction is discussed by using the calculated standard formation Gibbs energies of the reaction species at 298.15 K. The corresponding equilibrium constant as a function of temperature is found to be close to experimental values.
    Keywords: Equilibrium Constants ; Thermochemical Properties ; Ab-Initio Calculations ; Chemistry
    ISSN: 0021-9614
    E-ISSN: 1096-3626
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  • 9
    Language: English
    In: Bioconjugate chemistry, 21 December 2011, Vol.22(12), pp.2546-57
    Description: In this work, the photophysical properties of two oxazine dyes (ATTO 610 and ATTO 680) covalently attached via a C6-amino linker to the 5'-end of short single-stranded as well as double-stranded DNA (ssDNA and dsDNA, respectively) of different lengths were investigated. The two oxazine dyes were chosen because of the excellent spectral overlap, the high extinction coefficients, and the high fluorescence quantum yield of ATTO 610, making them an attractive Förster resonance energy transfer (FRET) pair for bioanalytical applications in the far-red spectral range. To identify possible molecular dye-DNA interactions that cause photophysical alterations, we performed a detailed spectroscopic study, including time-resolved fluorescence anisotropy and fluorescence correlation spectroscopy measurements. As an effect of the DNA conjugation, the absorption and fluorescence maxima of both dyes were bathochromically shifted and the fluorescence decay times were increased. Moreover, the absorption of conjugated ATTO 610 was spectrally broadened, and a dual fluorescence emission was observed. Steric interactions with ssDNA as well as dsDNA were found for both dyes. The dye-DNA interactions were strengthened from ssDNA to dsDNA conjugates, pointing toward interactions with specific dsDNA domains (such as the top of the double helix). Although these interactions partially blocked the dye-linker rotation, a free (unhindered) rotational mobility of at least one dye facilitated the appropriate alignment of the transition dipole moments in doubly labeled ATTO 610/ATTO 680-dsDNA conjugates for the performance of successful FRET. Considering the high linker flexibility for the determination of the donor-acceptor distances, good accordance between theoretical and experimental FRET parameters was obtained. The considerably large Förster distance of ~7 nm recommends the application of this FRET pair not only for the detection of binding reactions between nucleic acids in living cells but also for monitoring interactions of larger biomolecules such as proteins.
    Keywords: Fluorescence Resonance Energy Transfer ; Coloring Agents -- Chemistry ; DNA -- Chemistry ; Oligonucleotides -- Chemistry ; Oxazines -- Chemistry
    ISSN: 10431802
    E-ISSN: 1520-4812
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  • 10
    Language: English
    In: Journal of Physical Chemistry A, March 6, 2003, Vol.107(9), p.1405(6)
    Description: Multireference configuration interaction calculations of the low-lying excited states were carried out to obtain information about the electronic vertical spectrum up to excitation energies of about 6 eV from the ground state, including the transition dipole moments. The calculations demonstrate a similarity tithe from obtained results.
    Keywords: Excited State Chemistry -- Research ; Bromine Compounds -- Atomic Properties ; Photochemistry -- Research
    ISSN: 1089-5639
    Source: Cengage Learning, Inc.
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