Bringing time resolution to EXAFS: recent developments and application to chemical systems

The currently available methodologies for applying extended X-ray absorption fine structure (EXAFS) spectroscopy to the interrogation of dynamic chemical systems are critically reviewed. Particular regard is paid to applicable experimental timescales, extraction of structural information, sample presentation, and simultaneous pairing with complementary techniques; the potential for further developments in this area is also assessed.     

A two-component small molecule system for activity-based detection and signal amplification: application to the visual detection of threshold levels of Pd(II)

A detection and signal amplification strategy aimed toward threshold diagnostic assays for use in resource-limited settings is described. The strategy employs two small molecule reagents that work in tandem. One reagent detects a specific analyte, while the second amplifies a colorimetric readout autocatalytically. The strategy is demonstrated using palladium(II) as a model analyte.     

Tryptophan-BODIPY: a versatile donor-acceptor pair for probing generic changes of intraprotein distances

We demonstrate that Tryptophan (Trp) and N-(4,4-difluoro-5,7-dimethyl-4-bora-3a,4a-diaza-s-indacene-3-yl)methyl iodoacetamide (BODIPY) is a suitable donor-acceptor (D-A) pair for intraprotein distance measurements, applicable to the study of protein folding. The suitability of the Trp-BODIPY electronic energy transfer is exemplified on the extensively-characterised two-state protein, S6, from Thermus thermophilus. This protein has proved to be useful for the elucidation of folding cooperativity and nucleation, as well as the changes upon induction of structural transitions. For a comprehensive structural coverage, BODIPY molecules were anchored by Cys insertions at four different positions on the S6 surface. Trp residues at position 33 or 62 acted as donors of electronic energy to the BODIPY groups. None of the D-A pairs show any detectable difference in the folding kinetics (or protein stability), which supports the notion that the two-state transition of S6 is a highly concerted process. Similar results are obtained for mutants affecting the N- and C-terminus. The kinetic analyses indicate that changes of the transition state occur through local unfolding of the native state, rather than by a decrease of the folding cooperativity. The distances obtained from the analysis of the time-resolved fluorescence experiments in the native state were compared to those calculated from X-ray structure. As an additional measure, molecular dynamics simulations of the different protein constructs were performed to account for variability in the BODIPY location on the protein surface. The agreement between fluorescence and X-ray data is quite convincing, and shows that energy transfer measurements between Trp and BODIPY can probe distances between ca. 17 to 34 A, with an error better than 10%.     

Measurements of carbon to amide-proton distances by C-H dipolar recoupling with 15N NMR detection

A new magic-angle spinning NMR method for measuring internuclear distances between a 13C-labeled site and amide protons is described. The magnetization of the protons evolves under homonuclear decoupling and the recoupled 13C-1H dipolar interaction, which provides simple spin-pair REDOR curves if only one 13C-labeled site is present. The modulation of the amide proton HN is detected via short 1H-15N cross polarization followed by 15N detection. The method is demonstrated on two specifically 13C- and 15N-labeled peptides, with 13C-HN distances from 2.2 to ca. 6 A. This technique promises to be particularly useful for measuring distances between 13C=O and H-15N groups, to identify hydrogen bonds in peptides and proteins.     

Label-free detection of DNA mutations by SPR: application to the early detection of inherited breast cancer

A screening analysis of DNA hybridization and the presence of DNA mutations using an surface plasmon resonance (SPR) biosensor is shown. The influence of lateral and vertical spacers, as well as several hybridization conditions, was studied to optimize the differentiation between fully complementary and mismatched DNA strands. Our results demonstrated that SPR biosensors were able to detect mismatch sequences related to inherited breast cancer, with high specificity and sensitivity. Using PCR synthetic sequences as targets, mutant sequences were clearly discriminated from fully complementary ones, and detection limits below 50 nM were achieved.     

On the detection by EXAFS spectroscopy of multimeric species and of complex anions in diethylether and diethylcarbonate

EXAFS spectroscopy has been shown to be a reliable tool for detecting the formation in solutions of molecular associations (LiBr)_n where n is solvent dependent. The signal Br^*...Br observed at 3.8₇ Å confirms the formation of tetrameric species (n=4) in diethylether (Et₂O) but only of dimers (n=2) in diethylcarbonate. Another signal observed at 2.4₅ Å has·been attributed to the pair Br^*...Li. The study of Li₂MBr₄–Et₂O solutions (M=Co, Cu, Zn) also affords new evidence for the formation of complex anions MBr ₄ ^2– but the spectra obtained at the bromine or metalK-edges for LiZnBr₃–Et₂O solutions seems to indicate the formation of more complex aggregates (LiMBr₃)_q. While the signal of the shell Br^*...Br is found quite intense for the reference CBr₄–Et₂O system, it does not appear for the MBr ₄ ^2– complex except for CuBr ₄ ^2– where the Jahn-Teller effect might rigidify a distorted tetrahedral structure.Presented, in part, at the VIIth International Conference on Non-Aqueous Solutions, Regensburg, West Germany, Ausgust 1980.     

Study of the peak broadening due to detection in the electrophoretic separation of DNA by CE and microchip CE and the application of image sensor for ultra‐small detection cell length

Narrow peaks are important to high‐resolution and high‐speed separation of DNA fragments by capillary electrophoresis and microchip capillary electrophoresis. Detection cell length is one of the broadening factors, which is often ignored in experiments. However, is it always safe to neglect detection cell length under any condition? To answer this question, we investigated the influence of detection cell length by simulation and experiments. A parameter named as detection cell length ratio was proposed to directly compare the detection cell length and the spatial length of sample band. Electrophoretic peaks generated by various detection cell length ratios were analyzed. A simple rule to evaluate the peak broadening due to detection cell length was obtained. The current states of the detection cell length of detection system and their reliabilities in capillary electrophoresis and microchip capillary electrophoresis were analyzed. Microchip capillary electrophoresis detection with an ultra‐small detection cell length of 0.36 μm was easily achieved by using an image sensor.     

Headspace mass spectrometry methodology: application to oil spill identification in soils

In the present work we report the results obtained with a methodology based on direct coupling of a headspace generator to a mass spectrometer for the identification of different types of petroleum crudes in polluted soils. With no prior treatment, the samples are subjected to the headspace generation process and the volatiles generated are introduced directly into the mass spectrometer, thereby obtaining a fingerprint of volatiles in the sample analysed. The mass spectrum corresponding to the mass/charge ratios (m/z) contains the information related to the composition of the headspace and is used as the analytical signal for the characterization of the samples. The signals obtained for the different samples were treated by chemometric techniques to obtain the desired information. The main advantage of the proposed methodology is that no prior chromatographic separation and no sample manipulation are required. The method is rapid, simple and, in view of the results, highly promising for the implementation of a new approach for oil spill identification in soils. Figure PCA score plots illustrate clear discrimination of types of crude oil in polluted soil samples (e.g. results are shown for vertisol)     

Improved methodology for the preparation of water-soluble maleimide-functionalized small gold nanoparticles

Improved methodology to prepare maleimide-functionalized, water-soluble, small (<3 nm) gold nanoparticles using a retro-Diels-Alder strategy that we developed for similar organic-soluble AuNP's is described. Importantly, our results suggest that a recent paper by Zhu, Waengler, Lennox, and Schirrmacher describing a similar strategy gave results inconsistent with the formation of the titled maleimide-modified AuNP (Zhu, J.; Waengler, C.; Lennox, R. B.; Schirrmacher, R. Langmuir2012, 28, 5508) as the major product, but consistent with the major product being an adduct derived from the hydrolysis of maleimide formed under the conditions used for the required deprotection of the maleimide. Our methodology provides an efficient and accessible route to pure maleimide-modified small AuNP's that circumvents the formation of the hydrolysis product. The maleimide-modified small AuNP's are versatile because they are soluble in water and in a wide range of organic solvents and their reactivity can now be properly exploited as a reactive moiety in Michael addition for bioconjugation studies in aqueous solution.     

New application of the QuEChERS methodology for the determination of volatile phenols in beverages by liquid chromatography

The QuEChERS methodology has been used for the determination of pesticides in solid samples. However, this technique can be equally useful for other applications, namely for liquid samples.     

Statistical thermodynamics models for polyatomic adsorbates: application to adsorption of n-paraffins in 5A zeolite

Experimental adsorption isotherms of five n-paraffins (ethane, propane, butane, pentane, and hexane) in 5A zeolite were described by means of a statistical thermodynamics model for linear adsorbates (MLA) developed by Ramirez-Pastor et al. (1999) and compared with the well-known multisite Langmuir model (MSL) of Nitta et al. (1984). The experimental data, obtained by different authors in a wide range of temperatures and pressures, were correlated by using an algorithm of multiple fitting. Two main conclusions were drawn from the analysis of experimental data: (i) for small molecules (ethane, propane), MLA is the more accurate model, validating the hypothesis of the linear rigid character of the adsorbate and reinforcing previous results obtained from the analysis of computational experiments developed for dimers and linear trimers; (ii) for large molecules (n-butane, n-pentane, n-hexane), the better performance of the MSL model suggests that the admolecules adsorb in a nonlinear structure. The isosteric heat of adsorption dependence on the number of carbons obtained from our study, ranging between 23.84 kJ/mol for ethane and 59.26 kJ/mol for hexane, showed a very good agreement with previous results reported in the literature, confirming the consistency of our analysis.     

Assessment of Chinese medicinal herb metabolite profiles by UPLC-MS-based methodology for the detection of aristolochic acids

In this study, aristolochic acid in different herbal medicines containing a mixture of varying herb species was identified through fingerprint pattern similarities. Aristolochic acid I and II are nephrotoxic compounds naturally present in the Aristolochia plant species that are commonly used in Chinese herbal medicines. Twenty-four commercially available herbal formulations were extracted into an aqueous solution and injected into a UPLC-MS system. All the samples were analysed by multiple reaction monitoring (MRM) to check for the presence of aristolochic acids I and II. The same samples were then fingerprinted using two different gradient methods and the chromatograms deconvoluted into retention time (RT) and masses for the chemicals present taking concentration into account. Statistical analysis of this data revealed that samples were highly heterogeneous, and that the main differences between the preparations were concentrations of polar compounds. A model was constructed where the samples could be separated into two groups differentiated by the presence of the two forms of aristolochic acid.     

Spot test for the detection of iodate in the presence of periodate application to the detection of vic-dihydroxy compounds

Spot tests for the detection of 0.02 mug of iodate in the presence of 45 mg of periodate, and for the detection of 0.1 mug of vic-dihydroxy compounds are described. The tests are based on the iodide-iodate reaction, in the presence of periodate masked by an excess of molybdate.     

Site-selective EXAFS in mixed-valence compounds using high-resolution fluorescence detection: a study of iron in Prussian Blue

A quantitative analysis is presented for the site-selective Fe K-edge absorption spectra of Prussian Blue: Fe(4)[Fe(CN)(6)](3) x xH(2)O (x = 14-16). The site-selective spectra were recorded using high-resolution fluorescence detection of the K beta emission from a polycrystalline sample. The K beta fluorescence lines arising from the high-spin and low-spin sites are shifted in energy. Since the emission features partially overlap, fluorescence-detected absorption spectra using different emission energies represent different linear combinations of the pure high-spin and low-spin EXAFS. A numerical method was used to extract the individual site EXAFS spectra from the experimental data. The analysis yields a range of solutions. A unique solution can be obtained if homovalent model compounds are used to simulate the K beta fluorescence emission from the two Fe sites in Prussian Blue. EXAFS analysis of the range of spectra obtained in the numerical method yields almost identical interatomic distances for the different spectra while the Debye-Waller factors vary considerably. The distances obtained in the EXAFS fit correspond to the crystallographic distances.     

Recent developments in the methodology and application of MEEKC

MEEKC is an electrodriven separation technique that utilises the unique properties of a microemulsion (ME) as a background electrolyte to achieve separation of a diverse range of solutes. MEs are composed of nanometre-sized oil droplets suspended in aqueous buffer, which is commonly referred to as oil-in-water ME. The droplets are stabilised by the presence of both a surfactant and co-surfactant. The use of water-in-oil MEs in MEEKC has also been investigated. This review details the advances in MEEKC-based separations from the period June 2008 - June 2010. Areas covered include online sample concentration, suppressed electroosmosis MEEKC, chiral separations, MEEKC-MS, MEEKC-ICP-MS and ME structure characterisation. The review also includes a fundamental introduction to MEEKC, along with a review of recent applications.     

A methodology based on NIR-microscopy for the detection of animal protein by-products

This study develops a methodology based on NIR-microscopy analysis and chemometric tools for the detection of animal protein by-products in mixtures, such as compound feeds and mixtures of ingredients, using a library of animal meal by-products only. The proposed methodology is a two-step strategy which worked better than the SIMCA approach it was compared with. In the first step, animal particles are identified using one of two methods, a global or a local distance measure. In the second, K-nearest-neighbours (KNN) is used to discriminate between terrestrial and fish particles. The models were developed using a training set comprising 11,727 spectra of pure terrestrial meals and 5843 of fish meals. KNN using second derivative spectra and five neighbours correctly classifies 98.5% of these samples under cross-validation. The procedure was validated using two external datasets, one made up of mixtures of species (fish and bovine), and a second of commercial compound feeds. The results obtained confirm that the procedure is able to reliably detect the presence of animal meals, although further work would be needed to develop it into an accurate quantitative method.     

Program for predicting interatomic distances in crystals by the bond valence method

The program is a computer realization of the bond valence method (BVM), used to predict bond lengths in crystal structures from topological data. Using object-oriented programming made it possible to analyze structures of any complexity (up to 6480 crystal chemical positions). Hardware and software requirements: i486DX processor, operating system Windows 3.1/95, 4M RAM, and about 2M disk space. The program was developed at the Crystallography and Crystal Chemistry Department, Geological Faculty, Moscow State University. Translated fromZhumal Strukturnoi Khimii, Vol. 39, No. 4, pp. 708–713, July–August, 1998.     

Preparation of a biochip on porous silicon and application for label-free detection of small molecule-protein interactions

A new approach for the preparation of a biochip on porous silicon and the application of the biochip for detection of small molecule-protein interactions with desorption/ionization on porous silicon (DIOS) was demonstrated. The galvanostatically etched porous silicon substrates were chemically modified firstly to yield carboxylic acid terminated surfaces, and then the protein was covalently attached to the surface through amide bonding. By applying a solution of candidate chemicals to the surface and a subsequent wash step, the masses of captured compounds could be analyzed by DIOS. DIOS has advantages of being a direct detection tool compared to the classic fluorescence or chemiluminescence methods, because the process of labeling molecules employed in the fluorescence or chemiluminescence methods can sometimes alert the properties of the labeled molecule. The recognition between proteins and their binding partners is efficient and selective. A good tolerance to disturbance and high enrichment factor of the biochip to the analytes was observed. As an on-chip-based approach, the demonstrated method has a potential to perform in a high-throughput format.