Electrochemical Detection of TNT at Cobalt Phthalocyanine Mediated Screen‐Printed Electrodes and Application to Detection of Airborne Vapours

We describe the use of cobalt phthalocyanine as a mediator to improve the sensitivity for the electrochemical detection of TNT. Commercial screen‐printed electrodes containing cobalt phthalocyanine were employed for determination of TNT. Improved sensitivities compared to screen‐printed carbon electrodes without phthalocyanine were observed, current response for cyclic voltammetric measurements at modified electrodes being at least double that of unmodified electrodes. A synergistic effect between oxygen and TNT reduction was also observed. Correlation between TNT concentrations and sensor output was observed between 0–200 µM TNT. Initial proof‐of‐concept experiments combining electrochemical determinations, with the use of an air‐sampling cyclone, are also reported.     

FIPSDock: A new molecular docking technique driven by fully informed swarm optimization algorithm

The accurate prediction of protein–ligand binding is of great importance for rational drug design. We present herein a novel docking algorithm called as FIPSDock, which implements a variant of the Fully Informed Particle Swarm (FIPS) optimization method and adopts the newly developed energy function of AutoDock 4.20 suite for solving flexible protein–ligand docking problems. The search ability and docking accuracy of FIPSDock were first evaluated by multiple cognate docking experiments. In a benchmarking test for 77 protein/ligand complex structures derived from GOLD benchmark set, FIPSDock has obtained a successful predicting rate of 93.5% and outperformed a few docking programs including particle swarm optimization (PSO)@AutoDock, SODOCK, AutoDock, DOCK, Glide, GOLD, FlexX, Surflex, and MolDock. More importantly, FIPSDock was evaluated against PSO@AutoDock, SODOCK, and AutoDock 4.20 suite by cross‐docking experiments of 74 protein–ligand complexes among eight protein targets (CDK2, ESR1, F2, MAPK14, MMP8, MMP13, PDE4B, and PDE5A) derived from Sutherland‐crossdock‐set. Remarkably, FIPSDock is superior to PSO@AutoDock, SODOCK, and AutoDock in seven out of eight cross‐docking experiments. The results reveal that FIPS algorithm might be more suitable than the conventional genetic algorithm‐based algorithms in dealing with highly flexible docking problems. © 2012 Wiley Periodicals, Inc.     

Free‐energy differences between states with different conformational ensembles

Multiple conformations separated by high‐energy barriers represent a challenging problem in free‐energy calculations due to the difficulties in achieving adequate sampling. We present an application of thermodynamic integration (TI) in conjunction with the local elevation umbrella sampling (LE/US) method to improve convergence in alchemical free‐energy calculations. TI‐LE/US was applied to the guanosine triphosphate (GTP) to 8‐Br‐GTP perturbation, molecules that present high‐energy barriers between the anti and syn states and that have inverted preferences for those states. The convergence and reliability of TI‐LE/US was assessed by comparing with previous results using the enhanced‐sampling one‐step perturbation (OSP) method. A linear interpolation of the end‐state biasing potentials was sufficient to dramatically improve sampling along the chosen reaction coordinate. Conformational free‐energy differences were also computed for the syn and anti states and compared to experimental and theoretical results. Additionally, a coupled OSP with LE/US was carried out, allowing the calculation of conformational and alchemical free energies of GTP and 8‐substituted GTP analogs. © 2013 Wiley Periodicals, Inc.     

Two‐dimensional replica‐exchange method for predicting protein–ligand binding structures

We have developed a two‐dimensional replica‐exchange method for the prediction of protein–ligand binding structures. The first dimension is the umbrella sampling along the reaction coordinate, which is the distance between a protein binding pocket and a ligand. The second dimension is the solute tempering, in which the interaction between a ligand and a protein and water is weakened. The second dimension is introduced to make a ligand follow the umbrella potential more easily and enhance the binding events, which should improve the sampling efficiency. As test cases, we applied our method to two protein‐ligand complex systems (MDM2 and HSP 90‐alpha). Starting from the configuration in which the protein and the ligand are far away from each other in each system, our method predicted the ligand binding structures in excellent agreement with the experimental data from Protein Data Bank much faster with the improved sampling efficiency than the replica‐exchange umbrella sampling method that we have previously developed. © 2013 Wiley Periodicals, Inc.     

Automatic Headspace Sampling for Determination of Ethylene Dibromide Residues in Cereals

Abstract

The possibility was investigated to apply a commercially available automatic head-space sampler in trace analysis of ethylene dibromide (EDB, 1,2-dibromoethane), in cereals.

Samples of rice and wheat flour were thermostatted in closed vials at 70[ddot]C for 30min. The top gas was then automatically introduced into a gas chromatograph equipped with an electron capture detector. Quantitation was performed using external standards (untreated samples spiked with solutions of EDB in N,N′-dimethylacetamide).

The relative standard deviation of the method was 3.4% for rice and 4.5% for wheat flour, at a residue level of 0.008 mg/kg. The detection limit was 0.001 mg/kg (the official EC residue tolerance is 0.01 mg/kg).

Preliminary experiments with other fumigants were carried out as well.

The headspace technique in question has the following advantages over other methods for determining EDB residues in cereals: 1. No sample pre-treatment like extraction, steam distillation, purge and trap etc.; 2. Automated sample handling; 3. “Clean” chromatograms.     

Volatile organic compounds in an urban environment: a comparison among Belgium,Vietnam and Ethiopia

The effects of urban and indoor air pollution on human health are a major environmental concern for all, but not much has been researched in the developing world. Specifically, quantitative data on the occurrence of volatile organic compounds (VOCs) – main contributors to air pollution – in Asia and Africa are scarce compared to the availability of data in the developed world. This paper presents one of the first studies focusing on the analysis and occurrence of VOCs in Vietnam and Ethiopia, which constitutes part of the novelty of this work. A spectrum of 34 VOCs was measured at eight different urban sites in Ghent (Belgium), Hanoi (Vietnam), Jimma and Addis Ababa (Ethiopia) during three sampling campaigns from September 2008 to September 2010. Sampling was done in an active way by means of sorbent tubes filled with Tenax TA. The analysis was done by TD-GC-MS using internal standard calibration. Data were interpreted and compared in terms of (i) individual, subgroup and total VOCs concentration (TVOCs), (ii) indoor-to-outdoor (I/O) concentration ratios, (iii) source identification by diagnostic ratio and/or correlation coefficients, and (iv) ozone formation potential (OFP) at outdoor sites based on up-to-date maximum incremental reactivity (MIR). I/O concentration ratios varied between 0.2 and 30, with big differences noticed with respect to the type of VOC(s) considered and the type of outdoor sampling location. The highest TVOC concentrations were measured in street samples with maximum values of 54?µg/m³ in Ghent, 507?µg/m³ in Hanoi and 318?µg/m³ in Addis Ababa illustrating the large difference in ambient air quality levels. This is also reflected in the arithmetic mean OFP values (µg/m³) of 82, 1308 and 596 in Ghent, Hanoi and Addis Ababa, respectively. Results of this study could be helpful to support formulation of national policy with regard to ambient air quality.     

An improved Sampling Strategy for the Measurement of VOCs in Air,Based on Cooled Sampling and Analysis by Thermodesorption-GC-MS/FID

Abstract

Reliable and comprehensive sampling methods are required to obtain accurate data for VOC concentrations in air samples. The major drawback of the adsorption tube sampling method, widely employed in environmental studies, is the fact that C₂ compounds are usually not trapped quantitatively.

The focus of this work was thus to improve sampling based on adsorption tubes packed with Molsieve and Carbosieve. To improve the sampling efficiency for the C₂ compounds, a cooling device, based on Peltier cooling was constructed, which could be operated at a temperature down to ?30°C.

Experiments under laboratory and field conditions were carried out to study the influence of the sampling temperatuie on the recovery of ethane and ethene as the most volatile VOCs. The results clearly demonstrate the need for a cooled sampling device for the analysis of C₂ compounds in air. Under the investigated conditions, the recoveries with ambient temperature sampling were only in the range of 38–46% for ethane and 33–59% for ethene respectively, in comparison to the cooled sampling device. These findings are only valid for the described conditions and can change significantly with temperature and concentration. A generalisation of the recovery is thus very difficult to give.

The use of the sampling device for a field study is reported, where samples were collected simultaneously at three different altitudes in a diurnal profile on the slope of the Schulterberg mountain in Tyrol (Austria).     

Implementation of an adaptive umbrella sampling method for the calculation of multidimensional potential of mean force of chemical reactions in solution

We describe the implementation of an adaptive umbrella sampling method, making use of the weighted histogram analysis method, for computing multidimensional potential of mean force for chemical reaction in solution. The approach is illustrated by investigating the effect of aqueous solution on the free energy surface for the proton transfer reaction of [H(3)N-H-NH(3)](+) using a combined quantum mechanical and molecular mechanical AM1/TIP3P potential.     

High-dimensional model representations generated from low order terms--lp-RS-HDMR

High-dimensional model representation (HDMR) is a general set of quantitative model assessment and analysis tools for improving the efficiency of deducing high dimensional input-output system behavior. RS-HDMR is a particular form of HDMR based on random sampling (RS) of the input variables. The component functions in an HDMR expansion are optimal choices tailored to the n-variate function f(x) being represented over the desired domain of the n-dimensional vector x. The high-order terms (usually larger than second order, or equivalently beyond cooperativity between pairs of variables) in the expansion are often negligible. When it is necessary to go beyond the first and the second order RS-HDMR, this article introduces a modified low-order term product (lp)-RS-HDMR method to approximately represent the high-order RS-HDMR component functions as products of low-order functions. Using this method the high-order truncated RS-HDMR expansions may be constructed without directly computing the original high-order terms. The mathematical foundations of lp-RS-HDMR are presented along with an illustration of its utility in an atmospheric chemical kinetics model.     

ICP-AES detection of silicon carbide impurities volatilized in a graphite furnace with the use of carbon tetrachloride vapour

The analytical capability of high-temperature halogenation with carbon tetrachloride vapour in a graphite furnace was investigated for silicon carbide powder with known chemical composition and particle size. Intensity vs heating time curves were determined for analytical lines of Al, B, Ba, Ca, Cr, Cu, Fe, Mg, Mn, Ti, V and Si constituents, volatilized with and without the presence of CCl₄ vapour in the furnace atmosphere. Igniting 10 mg SiC at 2100 °C for 60 s in chlorinating atmosphere, the evaporated fraction of most of the constituents was higher than 90% (for Al about 50%). The line intensity vs sample mass (4–26 mg) relationships were linear for all impurities studied, while the intensity of silicon line showed a relatively small change with the sample mass. BEC (background equivalent concentration) values for this solid sampling technique (10 mg loaded sample) were 2–20 fold lower than those calculated for the conventional solution sample introduction method.