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.     

Effect of Discrete Macroion Charge Distributions on Electric Double Layer of a Spherical Macroion

The effect of replacing the conventional uniform macroion surface charge density with discrete macroion charge distributions on the structure of electric double layer (EDL) of a spherical macroion has been investigated by Monte Carlo (MC) simulations. Two discrete models have been investigated in addition to the central macroion charge: point charges localized on the macroion surface and finite-sized charges protruding into the solution. Both models have been studied with fixed and mobile macroion charges. The radial functions of local densities and electrostatic potential in EDL, are calculated and compared to the results obtained for the central macroion charge distribution. It is concluded that the model of charge distribution significantly affects the EDL structure close to the macroion, while the effect is much weaker at larger distances. With point charges localized on the macroion surface, counterions become stronger accumulated to the macroion, as a result the absolute values of surface potential ?₀ and zeta ξ potential are decreased. With protruding charges, the excluded volume effect dominates over the increased correlation ability; hence the counterions are less accumulated near the macroions and the absolute values of ?₀ and ξ potentials are increased.     

The Use of Various Chromatographic Techniques for the Determination of Phenylurea Herbicides and Their Corresponding Anilines in Environmental Samples,II. Applications

Abstract

In earlier work, various strategies have been developed for the trace-level determination of phenylurea herbicides and the anilines which are their main degradation products. They include catalytic hydrolysis of the phenylureas on silica, liquid chromatographic fractionation of complex mixtures of herbicides and anilines, derivatization of anilines and herbicides with electron-capture-sensitive reagents, and final analysis by means of capillary gas chromatography. In the present paper, the application of these principles to trace-level analysis of surface water, soil and crop samples is demonstrated.     

Determination of zinc in marine/lacustrine sediments by graphite furnace atomic absorption spectrometry using Pd/Mg chemical modifier and slurry sampling

Effectiveness of Pd/Mg chemical modifier for the accurate direct determination of zinc in marine/lacustrine sediments by graphite furnace atomic absorption spectrometry (GF-AAS) using slurry samples was evaluated. A calibration curve prepared by aqueous zinc standard solution with addition of Pd/Mg chemical modifier is used to determine the zinc concentration in the sediment. The accuracy of the proposed method was confirmed using Certified Reference Materials, NMIJ CRM 7303-a (lacustrine sediment) from National Metrology Institute of Japan, National Institute of Advanced Industrial Science and Technology, Japan, and MESS-3 (marine sediment) and PACS-2 (marine sediment) from National Research Council, Canada. The analytical results obtained by employing Pd/Mg modifier are in good agreement with the certified values of all the reference sediment materials. Although for NRC MESS-3 an accurate determination of zinc is achieved even without the chemical modifier, the use of Pd/Mg chemical modifier is recommended as it leads to establishment of a reliable and accurate direct analytical method. One quantitative analysis takes less than 15 minutes after we obtain dried sediment samples, which is several tens of times faster than conventional analytical methods using acid digested sample solutions. The detection limits are 0.13?µg?g^?1 (213.9?nm) and 16?µg?g^?1 (307.6?nm), respectively, in sediment samples, when 40?mg of dried powdered samples are suspended in 20?mL of 0.1?mol?L^?1 nitric acid and a 10?µl portion of the slurry sample is measured. The precision of the proposed method is 8–15% (RSD).     

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.     

Evaluation of Asphaltene Inhibitors Effect on Aggregation Coupled Sedimentation Process

The aggregation coupled sedimentation of asphaltene particles in toluene and heptanes mixture are investigated in the presence of two asphaltene inhibitors including, dodecyle resorcinol (DR) and hazelnut oil. An image processing technique is adopted in the three sections in a settling column setup. The aggregation and sedimentation phenomena are evaluated through a time-driven Monte Carlo (MC) model. The results are in good agreement with the obtained experimental results. The results indicate that in controlling asphaltene sedimentation DR is more effective. The results also revealed that the hazelnut oil has a capacity to inhibit asphaltene sedimentation at high concentration.     

Fitting formula for the injection volume of a gas chromatograph for radio‐xenon sampling in the lower troposphere

GC is usually used for xenon concentration and radon removal in the International Monitoring System of the Comprehensive Nuclear‐Test‐Ban Treaty. In a gas chromatograph, the injection volume is defined to calculate the column capacity. In this paper, the injection volume was investigated and a fitting formula for the injection volume was derived and discussed subsequently. As a consequence, the xenon injection volume exponentially decreased with the column temperature increased, but exponentially increased as the flow rate increased.     

Optimization of sampling frequency for routine river water quality monitoring

Sampling frequency is an important factor to be considered during the design of a water monitoring network,and the cost-effective selection of possible ways and means for the optimization of sampling frequency is still needed.This paper introduces water pollution index deviation ratio comparison(WPI DRC),a procedure for the optimization of sampling frequency for a routine river water quality monitoring system.Sampling frequency optimized using WPI DRC at monitoring station X5 in the mainstream of Xiangjiang River is compared with that established using the traditional Statistical Algorithm method.The result of comparison indicates that WPI DRC is more feasible than the traditional one.And then,the sampling frequencies for other 16 monitoring stations also have been optimized,and the results show the sampling frequencies of all the stations except that X4 are reduced,and there is no unacceptable difference between water quality evaluation results at 17 stations before and after the optimization.Therefore,it is concluded that WPI DRC is an effective optimization process with operable results,which can be used to fulfill the requirement of practical monitoring work.