Analytic models of domain-averaged Fermi holes: a new tool for the study of the nature of chemical bonds

Simple analytical models are introduced that significantly enhance the ability to understand and rationalise the nature of bonding interactions depicted by domain-averaged Fermi hole (DAFH) analysis. The examples presented show that besides shedding new light on the role of electron-sharing in ordinary two-centre two-electron (2c-2e) chemical bonds that are well represented by the classical Lewis model, the proposed approach also provides interesting new insights into the nature of bonding interactions that go beyond the traditional Lewis paradigm. This is, for example, the case of 3c-2e multicentre bonding, but a straightforward extension of the approach also reveals for direct metal-metal bonding the existence of a completely new type of bonding interaction that involves the mutual exchange of electrons between the lone pairs on adjacent metal atoms.     

Development of a strategy and process parameters for a green process in counter-current chromatography: purification of tanshinone IIA and cryptotanshinone from Salvia miltiorrhiza Bunge as a case study

A strategy for the development of a green process using counter-current chromatography technology is presented in this paper. The strategy began with solvent system selection, followed by linear scale-up from an analytical to a preparative process with optimized operating parameters. A two-stage separation using a multi-injection method was performed with a solvent system of hexane-dichloromethane-methanol-water (4:0.75:4:1) for the 1st stage and a hexane-ethanol-water (4:2:2) for the 2nd stage. A 191.8 mg of tanshinone IIA was purified, with a 97% purity and 34.4% recovery and a 276.7 mg of cryptotanshinone was separated, with a 95% purity and 31.8% recovery from 2.1g of crude extract. Process parameters (throughput, efficiency, environmental risk factor and general process evaluation) and mass factors (mass intensity, separation mass efficiency and greenness) of a target were developed for monitoring of the counter-current chromatography process.     

Response surface methodology in drug design: A case study on docking analysis of a potent antifungal fluconazole

Molecular docking is a valuable in silico technique for discovery/design of bioactive compounds. A current challenge within docking simulations is the incorporation of receptor flexibility. A useful strategy toward solving such problem would be the docking of a typical ligand into the multiple conformations of the target. In this study, a multifactor response surface model was constructed to estimate the AutoDock based binding free energy of fluconazole within multiple conformations of 14α-demethylase (CYP51) (cross docking) as a validated antifungal target. On the basis of developed models, individual and interactive effects of important experimental parameters on cross docking of fluconazole were elucidated. For this purpose, a set of high-resolution holo crystallographic structures from CYP51 of human pathogen Trypanosoma cruzi were retrieved to statistically model the binding mode and affinity of fluconazole. The changes of AutoDock binding free energy for the complexes of CYP51-fluconazole were elucidated with the simultaneous variations of six independent variables including grid size, grid spacing, number of genetic algorithm (GA) runs, maximum number of energy evaluations, torsion degrees for ligand and quaternion degrees for ligand. It was revealed that grid spacing (distance between adjacent grid points) and maximum number of energy evaluations were two significant model terms. It was also revealed that grid size, torsion degrees for ligand and quaternion degrees for ligand had insignificant effects on estimated binding energy while the effect of GA runs was non-significant. The interactive effect of “torsion degrees for ligand” with number of GA runs was found to be the significant factor. Other important interactive effects were the interaction of “number of GA runs” with “grid spacing” and “number of energy evaluations” with “grid size”. Furthermore; results of modeling studies within several CYP51 conformations exhibited that “number of GA runs” and “number of energy evaluations” were less sensitive to varied target conformations.     

On the usefulness of generalised quantum chemical valence parameters in monitoring the course of a chemical reaction: A case study of the photochemical decomposition of HNO in excited states

A variant of the orthogonal gradient method of orbital optimization in the INDO-MCSCF framework has been used to study the photochemical decomposition of the HNO molecule into H + NO in the lowest^1.3A″ states. A complete geometry optimization has been carried out at all points of the reaction path which appears to be almost barrierless. The one-electron density matrix extracted from the optimized wavefunction at each point has been used to generate the relevant sets of quantum chemical valence parameters. A sharp transition is noted in the N-H bond order and hydrogen free valence index when plotted as functions of r_NH. This enables us to locate the transition region easily.     

A new non-destructive method for chemical analysis of particulate matter filters: the case of manganese air pollution in Vallecamonica (Italy)

Total Reflection X-ray Fluorescence (TXRF) is a well-established technique for chemical analysis, but it is mainly employed for quality control in the electronics semiconductor industry. The capability to analyze liquid and uniformly thin solid samples makes this technique suitable for other applications, and especially in the very critical field of environmental analysis. Comparison with standard methods like inductively coupled plasma (ICP) and atomic absorption spectroscopy (AAS) shows that TXRF is a practical, accurate, and reliable technique in occupational settings. Due to the greater sensitivity necessary in trace heavy metal detection, TXRF is also suitable for environmental chemical analysis. In this paper we show that based on appropriate standards, TXRF can be considered for non-destructive routine quantitative analysis of environmental matrices such as air filters. This work has been developed in the frame of the EU-FP6 PHIME (Public Health Impact of long-term, low-level Mixed element Exposure in susceptible population strata) Integrated Project (www.phime.org). The aim of this work was to investigate Mn air pollution in the area of Vallecamonica (Italy).     

Measurement of permethrin,deltamethrin and malathion pesticide residues in the wheat flour and breads and probabilistic health risk assessment: a case study in Kermanshah,Iran

ABSTRACT

This study was conducted to investigate the residues of pyrethroid and organophosphorus pesticide in flour and breads which were collected from local markets in Kermanshah province, Iran. Four different types of breads and two types of flour samples with high distribution were taken from market and their residues of pesticides were measured. A simple dispersive liquid–liquid microextraction (DLLME) method with solidification of floating organic drop was developed for the measurement. The health risk of these pesticides on adults and children health was assessed by target hazard quotient (THQ) using Monte Carlo simulation (MCS) method. About, 15% and 11.1% of total samples contained detectable levels of deltamethrin and malathion, respectively. None of the tested samples showed any permethrin residue. The results from all samples showed that none of the pesticides exceeded the maximum residue limits (MRLs). About 85% of pesticide residue detections were observed in tropical and mild weather area which is due to high consumption rate of insecticides in these areas. The percentile 95% of THQ is due to bread ingestion content of deltamethrin which was 0.033 and 0.070 for the adults and children, respectively, while this value for malathion was found to be, 0.015 and 0.030, respectively. In the adults and children for both deltamethrin and malathion, the percentile 95% of THQ value were lower than 1 (acceptable level). The non-carcinogenic health risk assessment indicated that bread consumers in Kermanshah province are not at a considerable risk because of deltamethrin and malathion.     

Toward assessment of density functionals for vibronic coupling in two‐photon absorption: A case study of 4‐nitroaniline

In this study, we predict vibronic two‐photon absorption (TPA) spectra for 4‐nitroaniline in vacuo. The simulations are performed using density functional theory and the approximate second‐order coupled‐cluster singles and doubles model CC2. Thereby we also demonstrate the possibility of simulations of vibronic TPA spectra with ab initio wavefunction methods that include electron correlation for medium‐sized systems. A special focus is put on the geometric derivatives of the second‐order transition moment and the dipole moment difference between the charge‐transfer excited state and the ground state. The results of CC2 calculations bring new insight into the vibronic coupling mechanism in TPA spectra of 4‐nitroniline and demonstrate that the mixed term is quite large and that it also exhibits a negative interference with the Franck‐Condon contribution. © 2015 Wiley Periodicals, Inc.     

A strategy for extending the applicability of a validated plasma calibration curve to quantitative measurements in multiple tissue homogenate samples: a case study from a rat tissue distribution study of JI-101, a triple kinase inhibitor

A general practice in bioanalysis is that, whatever the biological matrix the analyte is being quantified in, the validation is performed in the same matrix as per regulatory guidelines. In this paper, we are presenting the applicability of a validated LC‐MS/MS method in rat plasma for JI‐101, to estimate the concentrations of JI‐101 in various tissues that were harvested in a rat tissue distribution study. A simple protein precipitation technique was used to extract JI‐101 and internal standard from the tissue homogenates. The recovery of JI‐101 in all the matrices was found to be >70%. Chromatographic separation was achieved using a binary gradient using mobile phase A (acetonitrile) and B (0.2% formic acid in water) at a flow rate of 0.30 mL/min on a Prodigy ODS column with a total run time of 4.0 min. The MS/MS ion transitions monitored were 466.1 → 265 for JI‐101 and 180.1 → 110.1 for internal standard. The linearity range was 5.02–4017 ng/mL. The JI‐101 levels were quantifiable in the various tissue samples harvested in this study. Therefore, the use of a previously validated JI‐101 assay in plasma circumvented the tedious process of method development/validation in various tissue matrices. Copyright © 2011 John Wiley & Sons, Ltd.     

Proficiency testing as a tool for implementing internal quality control: the case of ochratoxin A in cocoa powder

This paper describes the interlaboratory study aimed at assessing the performance of 18 laboratories (14 national and 4 European) for Ochratoxin A (OTA) determination in cocoa powder samples. The study was tested at three levels of OTA covering the range in which presumably European regulatory limits could fall in the near future. For the extraction step, almost all laboratories used an aqueous solution of sodium hydrogen carbonate with the exception of one laboratory using dichloromethane consistently with the ELISA procedure adopted in the study. The clean-up step was performed by utilizing the immunoaffinity columns by the two main manufacturers (R-Biopharm Rhone and VICAM) and for the quantitative analysis, HPLC was used by all the participants except one using ELISA. From the output of the study, it can be concluded that at low level (0.19 μg/kg) 10 out of 18 (56%), at medium level (0.45 μg/kg) 11 out of 18 (61%), and at high level (1.45 μg/kg) 12 out of 18 (67%) results fell within the satisfactory ranges. This interlaboratory study provides an estimate of the performance of national and European laboratories involved in OTA determination in cocoa powder samples, which sounds extremely valuable in view of potential future legislation by the European Commission.     

Molecular dynamics study of host–guest interactions in cyclodextrins: methodology and data analysis for a comparison with solution data and the solid-state structure

A general method is proposed to model the behavior of cyclodextrins (CDs) and of their inclusion compounds through energy minimizations and molecular dynamics (MD) simulations at a constant temperature. In this way, the formation of a host–guest compound is obtained starting from many trial geometries with the guest outside the CD cavity without any a priori assumption. The MD simulation results are analyzed through two functions: (i) the similarity maps of the root-mean-square distances between instantaneous conformations found in the MD runs to recognize different families of conformers; (ii) the pair distribution function PDF, yielding the probability density of finding appropriate atom pairs as a function of their distance at equilibrium. As an example, the inclusion compound formed by β-CD and (−)-menthol-β-d-glucoside is investigated. The lowest-energy inclusion compound is in good agreement with the results of single-crystal X-ray analysis, while at room temperature the MD runs show a closely similar arrangement with thermal fluctuations. In this case, the PDF between diagnostic hydrogen atoms of β-CD and of the guest molecule are fully consistent with the experimental NOE results obtained from NMR measurements in solution.     

Variable selection in visible/near infrared spectra for linear and nonlinear calibrations: A case study to determine soluble solids content of beer

Three effective wavelength (EW) selection methods combined with visible/near infrared (Vis/NIR) spectroscopy were investigated to determine the soluble solids content (SSC) of beer, including successive projections algorithm (SPA), regression coefficient analysis (RCA) and independent component analysis (ICA). A total of 360 samples were prepared for the calibration (n = 180), validation (n = 90) and prediction (n = 90) sets. The performance of different preprocessing was compared. Three calibrations using EWs selected by SPA, RCA and ICA were developed, including linear regression of partial least squares analysis (PLS) and multiple linear regression (MLR), and nonlinear regression of least squares-support vector machine (LS-SVM). Ten EWs selected by SPA achieved the optimal linear SPA-MLR model compared with SPA-PLS, RCA-MLR, RCA-PLS, ICA-MLR and ICA-PLS. The correlation coefficient (r) and root mean square error of prediction (RMSEP) by SPA-MLR were 0.9762 and 0.1808, respectively. Moreover, the newly proposed SPA-LS-SVM model obtained almost the same excellent performance with RCA-LS-SVM and ICA-LS-SVM models, and the r value and RMSEP were 0.9818 and 0.1628, respectively. The nonlinear model SPA-LS-SVM outperformed SPA-MLR model. The overall results indicated that SPA was a powerful way for the selection of EWs, and Vis/NIR spectroscopy incorporated to SPA-LS-SVM was successful for the accurate determination of SSC of beer.     

Improving the robustness of a partial least squares (PLS) model based on pure component selectivity analysis and range optimization: case study for the analysis of an etching solution containing hydrogen peroxide

Pure component selectivity analysis (PCSA) was successfully utilized to enhance the robustness of a partial least squares (PLS) model by examining the selectivity of a given component to other components. The samples used in this study were composed of NH₄OH, H₂O₂ and H₂O, a popular etchant solution in the electronic industry. Corresponding near-infrared (NIR) spectra (9000-7500 cm⁻¹) were used to build PLS models. The selective determination of H₂O₂ without influences from NH₄OH and H₂O was a key issue since its molecular structure is similar to that of H₂O and NH₄OH also has a hydroxyl functional group. The best spectral ranges for the determination of NH₄OH and H₂O₂ were found with the use of moving window PLS (MW-PLS) and corresponding selectivity was examined by pure component selectivity analysis. The PLS calibration for NH₄OH was free from interferences from the other components due to the presence of its unique NH absorption bands. Since the spectral variation from H₂O₂ was broadly overlapping and much less distinct than that from NH₄OH, the selectivity and prediction performance for the H₂O₂ calibration were sensitively varied depending on the spectral ranges and number of factors used. PCSA, based on the comparison between regression vectors from PLS and the net analyte signal (NAS), was an effective method to prevent over-fitting of the H₂O₂ calibration. A robust H₂O₂ calibration model with minimal interferences from other components was developed. PCSA should be included as a standard method in PLS calibrations where prediction error only is the usual measure of performance.     

A fast and accurate isotope dilution GC‐IT‐MS/MS method for determination of eugenol in different tissues of fish: Application to a depletion study in mandarin fish

An accurate, rapid and effective method was established for determination of eugenol in plasma, muscle, skin, liver, kidney and gill of fish using gas chromatography–ion trap tandem mass spectrometry. Samples of muscle, skin, liver, kidney and gill were prepared using the modified QuEChERS (quick, easy, cheap, effective, rugged and safe) procedure, and a plasma sample was prepared by a liquid–liquid extraction procedure. Eugenol was monitored in <7 min using an electron‐ionization source in MS/MS mode and quantified by an internal standard of eugenol‐d₃. The limit of detection was 5.0 μg/kg, and the limit of quantification was 10.0 μg/kg. The calibration curve was linear in the range of 5–1000 μg/L (R² = 0.9996). Intra‐ and inter‐day precisions of eugenol expressed as relative standard deviation were within 9.74%, and the accuracy exhibited a relative error ranging from −2.20 to 8.89%. The developed method was successfully used to study the elimination regularity of eugenol in mandarin fish.     

A rapid and sensitive LC–MS/MS method for analysis of iguratimod in human plasma: Application to a pharmacokinetic study in Chinese healthy volunteers

A rapid, sensitive and reproducible LC–MS/MS method was developed and validated to determine iguratimod in human plasma. Sample preparation was achieved by protein precipitation with acetonitrile. Chromatographic separation was operated on an Ultimate® XB‐C₁₈ column (2.1 × 50 mm, 3.5 μm, Welch) with a flow rate of 0.400 mL/min, using a gradient elution with acetonitrile and water which contained 2 mm ammonium acetate and 0.1% formic acid as the mobile phase. The detection was performed on a Triple Quad™ 5500 mass spectrometer coupled with an electrospray ionization interface under positive‐ion multiple reaction monitoring mode with the transition ion pairs of m/z 375.2 → 347.1 for iguratimod and m/z 244.3 → 185.0 for agomelatine (the internal standard), respectively. The method was linear over the range of 5.00–1500 ng/mL with correlation coefficients ≥0.9978. The accuracy and precision of intra‐ and inter‐day, dilution accuracy, recovery and stability of the method were all within the acceptable limits and no matrix effect or carryover was observed. As a result, the main pharmacokinetic parameters of iguratimod were as follows: C_max, 1074 ± 373 ng/mL; AUC_0–72, 13591 ± 4557 ng h/mL; AUC_0–∞, 13,712 ± 4613 ng h/mL; T_max, 3.29 ± 1.23 h; and t_1/2, 8.89 ± 1.23 h.     

Study of the GC–MS determination of the palmitic–stearic acid ratio for the characterisation of drying oil in painting: La Encarnación by Alonso Cano as a case study

The correct identification of drying oils plays an essential role in providing an understanding of the conservation and deterioration of artistic materials in works of art. To this end, this work proposes the use of peak area ratios from fatty acids after ensuring that the linear responses of the detector are tested. A GC-MS method, previously reported in the literature, was revisited to its developed and validated in order to identify and quantify of eight fatty acids that are widely used as markers for drying oils in paintings, namely myristic acid (C_14:0), palmitic acid (C_16:0), stearic acid (C_18:0), oleic acid (C_18:1), linoleic acid (C_18:2), suberic acid (2C₈), azelaic acid, (2C₉) and sebacic acid (2C₁₀). The quaternary ammonium reagent m-(trifluoromethyl)phenyltrimethylammonium hydroxide (TMTFAH) was used for derivatization prior to GC-MS analysis of the oils. MS spectra were obtained for each methyl ester derivative of the fatty acids and the characteristic fragments were identified. The method was validated in terms of calibration functions, detection and quantification limits and reproducibility using the signal recorded in SIR mode, since two of the methyl derivatives were not totally separated in the chromatographic run. The proposed method was successfully applied to identify and characterise the most widely used drying oils (linseed oil, poppy seed oil and walnut oil) in the painting La Encarnación. This 17th century easel painting is located in the main chapel of the cathedral in Granada (Spain) and was painted by the well-known artist of the Spanish Golden Age, Alonso Cano (1601-1667).