The reproducible normality of the crystallographic B-factor.

Reproducibility determines the utility of a measurement. In structural biology the reproducibility permeate areas such as mechanics, data measurement, data analysis and refinement. In order to access the reproducibility of the combined contribution of these sources in uncertainties of protein crystallography we evaluated four groups of parameters from data collection to final structural model. We used lysozyme as a model, with 20 datasets collected at 1.6 Å resolution using two dissimilar x-ray diffraction setups and refined through a single automatic pipeline without arbitrary interpretation. Besides statistical differences in some structural parameters, the reproducibility of the final refined models allowed the determination of positional uncertainty, in good agreement with the Luzzati coordinate error. While the raw B-factor was found non-reproducible, an empirical scaling/normalization resulted in reproducible B-factors. The validity of this empirical scaling was corroborated by the reproducibility of normalized B-factors of independently solved datasets from proteins (insulin and myoglobin) from varying space groups available from structural database. The reproducibility of normalized B-factor may reposition this displacement parameter in the analysis of chemical (ligands, pH) and physical (pressure, temperature, space groups) variables.

Intrinsic mobility of gaseous cationic and anionic aggregates of ionic liquids.

Travelling-wave ion mobility mass spectrometry was used to measure the intrinsic mobility of a series of gaseous supra-cation and supra-anion aggregates of several ionic liquids. Close mobilities were observed in a T-wave cell filled with helium at ca. 0.8 mbar for [(DAI)(n+1)(X)(n)](+) (DAI is the 1,3-dialkylimidazolium cation and X is the anion) as compared to the respective anions [(DAI)(n)(X)(n+1)](-) for n=0 to 9. The anomalous behavior reported before in the condensed phase seems therefore to be related to the unique structural organization of pure ionic liquids that provides both polar and non-polar regions with directionality in which the anionic species are more retained than the cationic species in the salt network.

Chemical profile of meta-chlorophenylpiperazine (m-CPP) in ecstasy tablets by easy ambient sonic-spray ionization, X-ray fluorescence, ion mobility mass spectrometry and NMR.

Meta-chlorophenylpiperazine (m-CPP) is a new illicit drug that has been sold as ecstasy tablets. Easy ambient sonic-spray ionization mass spectrometry (EASI-MS) and X-ray fluorescence spectrometry (XRF) are shown to provide relatively simple and selective screening tools to distinguish m-CPP tablets from tablets containing amphetamines (mainly 3,4-methylenedioxymethamphetamine (MDMA)). EASI-MS detects the active ingredients in their protonated forms: [m-CPP + H](+) of m/z 197, [MDMA + H](+) of m/z 194, and [2MDMA + HCl + H](+) of m/z 423 and other ions from excipients directly on the tablet surface, providing distinct chemical fingerprints. XRF identifies Cl, K, Ca, Fe, and Cu as inorganic ingredients present in the m-CPP tablets. In contrast, higher Cl concentrations and a more diverse set of elements (P, Cl, Ca, Fe, Cu, Zn, Pt, V, Hf, Ti, Pt, and Zr) were found in MDMA tablets. Principal component analysis applied to XRF data arranged samples in three groups: m-CPP tablets (four samples), MDMA tablets (twenty three samples), and tablets with no active ingredients (three samples). The EASI-MS and XRF techniques were also evaluated to quantify m-CPP in ecstasy tablets, with concentrations ranging from 4 to 40 mg of m-CPP per tablets. The m-CPP could only be differentiated from its isomers (o-CPP and for the three isomers p-CPP) by traveling wave ion mobility mass spectrometry and NMR measurements.

Analysis of biodiesel and biodiesel-petrodiesel blends by high performance thin layer chromatography combined with easy ambient sonic-spray ionization mass spectrometry.

High performance thin layer chromatography (HPTLC) combined with on-spot detection and characterization via easy ambient sonic-spray ionization mass spectrometry (EASI-MS) is applied to the analysis of biodiesel (B100) and biodiesel-petrodiesel blends (BX). HPTLC provides chromatographic resolution of major components whereas EASI-MS allows on-spot characterization performed directly on the HPTLC surface at ambient conditions. Constituents (M) are detected by EASI-MS in a one component-one ion fashion as either [M + Na](+) or [M + H](+). For both B100 and BX samples, typical profiles of fatty acid methyl esters (FAME) detected as [FAME + Na](+) ions allow biodiesel typification. The spectrum of the petrodiesel spot displays a homologous series of protonated alkyl pyridines which are characteristic for petrofuels (natural markers). The spectrum for residual or admixture oil spots is characterized by sodiated triglycerides [TAG + Na](+). The application of HPTLC to analyze B100 and BX samples and its combination with EASI-MS for on-spot characterization and quality control is demonstrated.

Single-shot biodiesel analysis: nearly instantaneous typification and quality control solely by ambient mass spectrometry.

Using a simple and easily implemented desorption/ionization mass spectrometry technique, a tiny droplet of biodiesel placed on the surface of a sheet of paper is analyzed directly and nearly instantaneously under ambient conditions. No pre-separation or sample preparation is required, and clean mass spectra are obtained with great simplicity. In the positive ion mode, easy ambient sonic-spray ionization mass spectrometry, EASI(+)-MS, provides typical profiles of the major components of biodiesel samples, that is, either methyl esters (FAME) or ethyl esters (FAEE) of the natural fatty acids and triglycerides (TAG) from residual oil or oil from adulteration. Each FAME (FAEE) or TAG molecule is detected as a single sodiated molecule, [M + Na] (+) with relative intensities that correlate well with the known fatty acid profiles of the oil. Using EASI(-)-MS, typical and complementary profiles of free fatty acids (FFA) are obtained, which are detected in their deprotonated forms [FAA - H] (-). A general, single-shot approach for biodiesel analysis is therefore described, and samples from different feedstocks, from blends with petrodiesel, or from either methanol or ethanol trans-esterification are readily typified and major parameters of quality accessed.

Structural analysis and Fourier transform infrared and Raman spectra of dibutoxyphosphoryl benzylisothiourea.

A structural analysis for dibutoxyphosphoryl benzylisothiourea (DBBT) was carried out by mass spectrometry, 1H NMR, 13C NMR, infrared and Raman spectroscopy. The Fourier transform infrared and Fourier transform Raman spectra of liquid of DBBT were carried out with the purpose of studying the tautomerism (structures I and II) and the behavior of the more polar absorption's bands in different solvents, i.e., absorption's of the P=O and C=N bands. The results suggest the existence of tautomerism in the pure (liquid) compound and in solution of CHCl(3), CH(2)Cl(2), CHBr(3), and THF, C(2)H(4)Cl(2) and C(2)H(4)Br(2). The solvent interaction with the P=O band was characterized by the presence of a new band in the region of the O-H absorption. A vibrational assignment of the IR bands and Raman shifts was done and is proposed in this paper.

Vibrational study of dialkylphosphonates: di-n-propyl- and di-i-propylphosphonates by semiempirical and ab initio methods.

Fourier transform infrared and Fourier transform Raman spectra of n-C(3)H(7) and i-C(3)H(7) dialkylphosphonates have been obtained. Semiempirical AM1 and the ab initio orbital molecular RHF/6-31G* theories have been used to study the molecular geometry, and the harmonic vibrational spectra with the purpose to assist the experimental assignments of these compounds. An extensive discussion on the assignment of the C-C, C-O, P-O and P=O stretching is carried out based on experimental data of compounds which have the propyl and isopropyl groups, as well as comparing the vibrational spectra of propane. Most of the RHF/6-31G* and AM1 results, once applied the appropriate scaling factor, showed an excellent agreement with the experimental wavenumbers. A few calculated frequencies related to CC and CO stretching do not agree well with the experimental trends.

Determination of PAHs: a practical example of validation and uncertainty assessment.

The objective of this study was to present a reliable and practical example of method validation and uncertainty assessment with an analytical method for the determination of polycyclic aromatic hydrocarbons (PAHs) in urban dust. The method was gas chromatography-mass spectrometry in combination with isotope dilution principle to achieve better accuracy for the results. The method performance parameters for five PAHs were determined (phenanthrene, fluoranthene, benzo[a]anthracene, benzo[a]pyrene and benzo[ghi]perylene); this method was used in the key comparison of CCQM-K50b for PAHs in particulate matter. The limits of detection and quantification were lower than 0.075 and 0.250 µg/g, respectively. The linear correlation coefficients were greater than 0.99. The major uncertainty contributions resulted from the accuracy of each analyzed PAH and the repeatability of the process. Certified reference material (National Institute of Standards and Technology SRM 1649a, urban dust) was used to determine the accuracy and precision of the method. The obtained results were satisfactory and agreed with all evaluated performance parameters.

Analysis of fuels via easy ambient sonic-spray ionization mass spectrometry.

The desorption and ionization of analytes directly from surfaces or natural matrices under ambient conditions has greatly simplified chemical analysis by mass spectrometry. Among the currently available set of such techniques, easy ambient sonic-spray ionization (EASI) is one of the simplest and most easily implemented. Fuels are among the most important and most complex classes of chemical mixtures and a challenge for fast and comprehensive chemical analysis. This review summarizes the applications of EASI-MS for fast, simple and nearly sample-preparation-free analysis of various fuels, focusing in typification, adulteration and quality control.