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.     

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.     

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.     

悬浮聚合制备大尺寸梭形聚苯乙烯粒子新方法及机理研究

利用氢氧化钾对苯乙烯-马来酸酐交替共聚物(SMA)进行水解,所得中等皂化程度的SMA水解产物(SMAA)在水溶液中具有刚性棒状直链构型;将此特殊结构的大分子作为分散剂用于苯乙烯悬浮聚合,通过控制搅拌速度和油水比,可得到梭形聚苯乙烯粒子;在优化条件下,粒子平均长度6.8 mm,宽度1.4 mm,厚度0.5 mm,长径比约5.0.其可能的机理为,中等皂化程度的刚棒直链型SMAA在聚合物"软粒子"表面能形成难以"回复"的有效保护层,使由剪切形成的变形聚合物"软粒子"在聚合过程中能保持形状和尺寸的稳定,从而得到梭形聚合物粒子.     

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.     

Application of accelerated heteronuclear single quantum coherence experiments to the rapid quantification of monosaccharides and disaccharides in dairy products

Monosaccharides and disaccharides are important dietary components, but if insufficiently metabolized by some population subgroups, they are also linked to disease patterns. Thus, the correct analytical identification, quantification, and labeling of these food components are crucial to inform and potentially protect consumers. Enzymatic assays and high-performance anion-exchange chromatography with pulsed amperometric detection are established methods for the quantification of monosaccharides and disaccharides that, however, require long measuring times (60–180 min). Accelerated methods for the identification and quantification of the nutritionally relevant monosaccharides and disaccharides d -glucose, d -galactose, d -fructose, sucrose, lactose, and maltose were therefore developed. To realize this goal, the NMR experiments HSQC (heteronuclear single quantum coherence) and acceleration by sharing adjacent polarization (ASAP)-HSQC were applied. Measurement times were reduced to 27 and 6 min, respectively, by optimizing the interscan delay and applying non-uniform sampling. The optimized methods were used to quantify d -glucose, d -galactose, d -fructose, sucrose, and lactose in various dairy products. Results of the HSQC and ASAP-HSQC methods are equivalent to the results of the reference methods in terms of both precision and accuracy, demonstrating that these methods can be used to correctly analyze nutritionally relevant monosaccharides and disaccharides in short times.     

Siloxanes in Biogas: Approaches of Sampling Procedure and GC-MS Method Determination

A new approach of siloxane sampling based on impinger, micro-impinger, adsorption on active carbon, and direct TedlarBag methods followed by gas chromatography-mass spectrometry (GC-MS) was developed for the analysis of three linear (L2–L4) and four cyclic (D3–D5) volatile methyl siloxanes (VMSs). Three kinds of organic liquid-medium characterized by different polarities, namely acetone, methanol, and d-decane as siloxanes trap were arranged in the experiment which is widely discussed below. Thus, the GC-MS equipped with SUPELCOWAX-10 capillary column was employed to perform monitoring of VMS content in the analyzed biogas samples originating from landfill, wastewater treatment plants, and agriculture biogas plants. In all samples that have undergone the analysis, cyclic and linear VMSs were found in quantities exceeding 107.9 and 3.8 mg/m³, respectively. Significant differences between siloxanes concentrations depending on biogas origin were observed. Moreover, the high range of linearity (0.1 to 70.06 mg/m³), low LoD (0.01 mg/m³), low LoQ (0.04 mg/m³), and high recovery (244.1%) indicate that the procedure and can be applied in sensitive analyses of silica biogas contaminants. In addition to the above, the impinger method of sampling performed better than active-carbon Tube and TedlarBag, particularly for quantifying low concentrations of siloxanes. Overall, the evaluation of sampling methods for biogas collection simplified the analytical procedure by reducing the procedural steps, avoiding the use of solvents, as well as demonstrated its applicability for the testing of biogas quality.