Toward theoretical analysis of long-range proton transfer kinetics in biomolecular pumps

Motivated by the long-term goal of theoretically analyzing long-range proton transfer (PT) kinetics in biomolecular pumps, researchers made a number of technical developments in the framework of quantum mechanics-molecular mechanics (QM/MM) simulations. A set of collective reaction coordinates is proposed for characterizing the progress of long-range proton transfers; unlike previous suggestions, the new coordinates can describe PT along highly nonlinear three-dimensional pathways. Calculations using a realistic model of carbonic anhydrase demonstrated that adiabatic mapping using these collective coordinates gives reliable energetics and critical geometrical parameters as compared to minimum energy path calculations, which suggests that the new coordinates can be effectively used as reaction coordinate in potential of mean force calculations for long-range PT in complex systems. In addition, the generalized solvent boundary potential was implemented in the QM/MM framework for rectangular geometries, which is useful for studying reactions in membrane systems. The resulting protocol was found to produce water structure in the interior of aquaporin consistent with previous studies including a much larger number of explicit solvent and lipid molecules. The effect of electrostatics for PT through a membrane protein was also illustrated with a simple model channel embedded in different dielectric continuum environments. The encouraging results observed so far suggest that robust theoretical analysis of long-range PT kinetics in biomolecular pumps can soon be realized in a QM/MM framework.     

A new approach to liquid penetrant inspection: radiolabeled QDots

Penetrant technique is a sensitive non-destructive testing (NDT) method for detecting and locating the presence of cracks in sample surface. Today, NDT is used in a wide range of industries including aerospace, biotechnology, defence, marine, oil–gas and energy plants. This work focuses on potential use of radiolabeled ZnS coated CdTe quantum dots (QDots) as a penetrant for liquid penetrant testing. The synthesized QDots as a precursor were tested for surface defects detection in welded joints. The experimental results show the highest activities were found in defects on the sample surface. These finding are consistent with the sample NDT inspection test report.     

Proficiency testing in analytical chemistry, microbiology and laboratory medicine: working discussions on current practice and future directions

A summary of the working group (WG) discussions on proficiency testing (PT) and external quality assessment (EQA) held at the Eurachem Workshop, Rome, 5–7 October 2008 is provided. The eight WG’s covered a range of issues concerned with current practice and future directions; how frequently should laboratories participate in PT/EQA? (WG1); developments in PT/EQA within the EU—what is required in future? (WG2); what issues do developing countries face with regards to PT/EQA? (WG3), what issues are specific to microbiology PT/EQA? (WG4); what new fields are emerging for PT/EQA? (WG5); what will be the impact of the new ISO/IEC 17043 standard? (WG6); do current PT/EQA schemes meet the needs of participants? (WG7); and what are the issues that affect the quality of proficiency test items? (WG8). Delegates with different backgrounds were on each WG in order to capture a range of views and experience from a number of different sectors. Working group representatives included PT/EQA providers, participants in PT/EQA schemes and end users of PT results such as accreditation bodies and regulatory authorities, from countries around the world.     

Unique emission from norbornene derived terpyridine--a selective chemodosimeter for G-type nerve agent surrogates

A new chemodosimeter for a G-type agent that exploits norbornene derived terpyridine (NDT)-lanthanide unique emission is reported. The unusual emission between terpyridine and norbornene motifs of NDT is attributed to the significant difference in the position of the HOMO and LUMO wave functions that prevents the non-radiative relaxation pathway. An interesting magenta emission from NDT along with Eu(III) is utilized as a new fluorometric chemodosimeter that selectively detects (by changing the observed magenta emission to blue) G-type agent surrogates. A detection limit of 40 ppb is obtained and the selectivity for reactive surrogates over a variety of other close chemical analogs is demonstrated.     

Contrôle non destructif de matériaux composites par la technique des courants de foucault : une nouvelle approche

Quality testing of composite materials is regularly carried out using non-destructive testing (NDT) techniques such as ultrasound, radiography or infrared thermography. However, these techniques present some limitations for the NDT of composites in terms of accuracy, sensitivity, repeatability of the signal and sometimes difficulty of calibration. In this article, it is demonstrated that eddy current testing, once solely dedicated for NDT of metallic materials, can also be adapted for the examination of composite materials. Indeed, this technique appears to be adequate for the detection and the characterisation of major flaws such as delamination and impact. A good reproducibility of the signals has been observed and this technique may become an efficient and low cost alternative compared to more complex and expensive techniques. Experimental results are shown and analysed and the advantages and limitations of eddy current testing of composite materials are discussed.     

Proficiency testing in analytical chemistry, microbiology and laboratory medicine: working discussions on current practice and future directions

A summary of the working group (WG) discussions on proficiency testing (PT) and external quality assessment (EQA) held at the EURACHEM Workshop, Istanbul, 3?C6 October 2011, is provided. The six WGs covered a range of issues concerned with current practice and future directions; implementing the requirements of ISO/IEC 17043 by PT/EQA providers (WG1); accrediting PT/EQA providers to ISO/IEC 17043 (WG2); pre- and post-analytical aspects in PT/EQA (WG3); evaluating participant performance in qualitative PT/EQA schemes (WG4); establishing PT/EQA schemes in developing countries (WG5); and establishing acceptability criteria in microbiology PT/EQA schemes (WG6). Delegates with different backgrounds were on each WG in order to capture a range of views and experience from a number of different sectors. Working group representatives included PT/EQA providers, participants in PT/EQA schemes and end-users of PT results such as accreditation bodies and regulatory authorities, from countries around the world.     

Proficiency testing in analytical chemistry, microbiology and laboratory medicine: working group discussions on current practice and future directions

A summary of the working group (WG) discussions on proficiency testing (PT) and external quality assessment (EQA) held at the joint EURACHEM/CITAC/EQALM workshop, Bracknell, UK, 16–18 February 2003 is provided. The nine WGs covered a range of issues concerned with current practice and future directions; PT/EQA as a tool for regulators (WG1); PT/EQA as a tool for accreditation (WG2); evaluation of performance and uncertainty (WG3); frequency of PT/EQA participation (WG4); selection of appropriate PT/EQA schemes (WG5); added value of PT/EQA and cost benefit evaluation (WG6); global harmonisation and rationalisation (WG7); new technical areas and challenges in PT/EQA (WG8); and accreditation of PT/EQA providers (WG9). Participants with different backgrounds were on each WG in order to capture a range of views and experience from different sectors. The discussions reflected on the keynote lectures and built, in many cases, on discussions at previous workshops in 2000 and 2002.     

Phase transfer membrane supported liquid-liquid-liquid microextraction combined with large volume sample injection capillary electrophoresis-ultraviolet detection for the speciation of inorganic and organic mercury

In this paper, a novel sample pretreatment technique termed phase transfer based liquid-liquid-liquid microextraction (PT-LLLME) was proposed for the simultaneous extraction of inorganic and organic mercury species. In PT-LLLME, an intermediate solvent (acetonitrile) was added into the donor phase to improve the contacting between target mercury species and complexing reagent. Meanwhile, a membrane supported (MS)-LLLME unit was designed to realize the PT-LLLME procedure. By using nylon membrane as supporting carrier, larger than 50 μL of acceptor solution could be hung up. Following PT/MS-LLLME, the acceptor solutions were directly analyzed by large volume sample stacking capillary electrophoresis/ultraviolet detection (LVSS-CE/UV). Accordingly, a new method of PT/MS-LLLME combined with LVSS-CE/UV was developed for the simultaneous speciation of inorganic and organic mercury species. Parameters affecting the extraction efficiency of PT/MS-LLLME were investigated in details. Under the optimized conditions, enrichment factors (EFs) ranging from 160- to 478-fold were obtained for the extraction of target mercury species by PT/MS-LLLME. By combining PT/MS-LLLME with LVSS-CE/UV, EFs were magnified up to 12,138-fold and the limits of detection (at a signal-to-noise ratio of 3) were at sub ppb level. The established approach of PT/MS-LLLME-LVSS-CE/UV was successfully applied to simultaneous determination of inorganic and organic mercury species in biological samples and environmental water samples.     

对硫磷在纳米氧化铝薄膜修饰电极上的电化学行为及其测定

制备了纳米氧化铝修饰玻碳电极(nano-Al2O3/GCE/CME),用循环伏安法(CV)、线性扫描伏安法(LSV)研究了对硫磷(TP)在nano-Al2O3/GCE/CME上的电化学行为.实验表明,该修饰电极与裸电极相比能显著提高TP的氧化还原峰电流并降低其氧化峰电位.在0.1 mol/L HAc-NaAc缓冲溶液(pH =5)中,TP在该修饰电极上产生1个不可逆的还原峰( Epc1=-0.567 V)和1对可逆氧化还原峰( Epa2=0.018 V和Epc2=-0.008 V) ,氧化峰电流与TP的浓度在2.5×10-9～1.0×10-7 mol/L和1.0×10-7～1.0×10-5 mol/L范围内具有良好的线性关系,回归方程分别为: ip(μA)=0.2529+4.201C(μmol/L), r=0.9984和ip(μA)=0.6752+0.3181C(μmol/L), r=0.9946.开路富集30 s后,检出限为1.0 ×10-9 mol/L(S/N=3).在1.0×10-5 mol/L TP试液中连续测定10次,其RSD为3.8%.用此方法测定了蔬菜中TP的含量,回收率为95. 6%～100.5% ,结果满意.     

Impact of isomeric structures on transistor performances in naphthodithiophene semiconducting polymers

Four isomeric naphthodithiophenes (NDTs) with linear and angular shapes were introduced into the polythiophene semiconductor backbones, and their field-effect transistor performances were characterized. The polymers bearing naphtho[1,2-b:5,6-b']dithiophene (NDT3), an angular-shaped NDT, exhibited the highest mobilities of ～0.8 cm(2) V(-1) s(-1) among the four NDT-based polymers, which is among the highest reported so far for semiconducting polymers. Interestingly, the trend of the mobility in the NDT-based polymers was contrary to our expectations; the polymers with angular NDTs showed higher mobilities than those with linear NDTs despite the fact that naphtho[2,3-b:6,7-b']dithiophene (NDT1), a linear-shaped NDT, has shown the highest mobility in small-molecule systems. X-ray diffraction studies revealed that angular-NDT-based polymers gave the highly ordered structures with a very close π-stacking distance of 3.6 ?, whereas linear-NDT-based polymers had a very weak or no π-stacking order, which is quite consistent with the trend of the mobility. The nature of such ordering structures can be well understood by considering their molecular shapes. In fact, a linear NDT (NDT1) provides angular backbones and an angular NDT (NDT3) provides a pseudostraight backbone, the latter of which can pack into the highly ordered structure and thus facilitate the charge carrier transport. In addition to the ordering structure, the electronic structures seem to correlate with the carrier transport property. MO calculations, supported by the measurement of ionization potentials, suggested that, while the HOMOs are relatively localized within the NDT cores in the linear-NDT-based polymers, those are apparently delocalized along the backbone in the angular-NDT-based polymers. The latter should promote the efficient HOMO overlaps between the polymer backbones that are the main paths of the charge carrier transport, which also agrees with the trend of the mobility. With these results, we conclude that angular NDTs, in particular NDT3, are promising cores for high-performance semiconducting polymers. We thus propose that both the molecular shapes and the electronic structures are important factors to be considered when designing high performance semiconducting polymers.     

Analysis of organomercury compounds in sediments by capillary GC with atomic fluorescence detection

Analysis of methyl- and ethylmercury (MM and EM) halides in biological and environmental samples is generally performed by gas chromatography with electron capture detection. Tedious sample work-up protocols and poor chromatographic response (using packed columns) have, however, shown the need for the development of new methods in this field. This paper reports a sensitive method, free from these deficiencies, for the determination of methyl- and ethylmercury. The organomercury compounds (MM and EM) are first released from the sample matrix, by the combined action of acidic potassium bromide and cupric ions, and then extracted into dichloromethane. The initial extracts are subjected to thiosulfate clean-up and the organomercury species are isolated as their chloride derivatives by addition of cupric chloride, and subsequent extraction into a small volume of organic solvent. Capillary GC coupled with atomic fluorescence detection provided excellent separation efficiencies for methyl- and ethylmercury and proved to be a very selective and sensitive technique. The absolute detection limit for both MM and EM was found to be 0.2 pg.     

Rapid discrimination of single-nucleotide mismatches using a microfluidic device with monolayered beads

A microfluidic device incorporating monolayered beads is developed for the discrimination of single-nucleotide mismatches, based on the differential dissociation kinetics between perfect match (PM) and mismatched (MM) duplexes. The monolayered beads are used as solid support for the immobilization of oligonucleotide probes containing a single-base variation. Target oligonucleotides hybridize to the probes, forming either PM duplexes or MM duplexes containing a single mismatch. Optimization studies show that PM and MM duplexes are easily discriminated based on their dissociation but not hybridization kinetics under an optimized buffer composition of 100 mM NaCl and 50% formamide. Detection of single-nucleotide polymorphism (SNP) using the device is demonstrated within 8 min using four probes containing all the possible single-base variants. The device can easily be modified to integrate multiplexed detection, making high-throughput SNP detection possible.     

Naphthodithiophene-based donor materials for solution processed organic solar cells

As an emerging donor building block, naphthodithiophene (NDT) is causing more concerns in the field of organic semiconductors. With the rigid and coplanar molecule structure, NDT will exhibit more application space relying on its own advantage for facilitating the charge carrier transport. In this review article, we have summarized the development progress on the NDT-based donor materials for solution processed organic solar cells. Discussions and comments on those representative NDT type materials about structure and property are also presented.     

Highly sensitive detection of melamine and its derivatives by capillary electrophoresis coupled with online preconcentration techniques

Two kinds of online preconcentration techniques including large-volume sample stacking-sweeping and selective-exhaustive injection-sweeping (SEI-S) were employed in CE to develop a rapid, simple and sensitive method for determination of melamine (MM) and its derivatives such as ammeline (AMN), ammelide (AMD) and cyanuric acid (CA) in liquid milk products. Though the sensitivity of large-volume sample stacking-sweeping is not particularly high, it can be used to detect all the four compounds simultaneously. However, it is very difficult to improve the sensitivity of these four compounds by using single SEI-S method directly, owing to their completely different extents of protonation or deprotonation. Grouping can solve this problem perfectly. After the four compounds are divided into two groups (MM/AMN and AMD/CA), cation-SEI-S or anion-SEI-S can be applied for their online stacking. In cation-SEI-S, the detection limits for MM and AMN were both 0.01 ng/mL based on the signal-to-noise ratio of 3. In anion-SEI-S, the detection limits were 0.05 and 0.02 ng/mL for CA and AMD, respectively. Results of this study show a great potential for the SEI-S method to be a useful tool for the rapid and sensitive determination of MM and its derivatives in liquid milk products.     

Purge and trap/thermal desorption device for the determination of dimethylselenide and dimethyldiselenide

A method is described for the determination of dimethylselenide and dimethyldiselenide using a purge-and-trap/thermal desorption device (PT/TD) coupled to a capillary column gas chromatograph with a six-way Valco valve. The system is constructed in such a way that it allows also on-column injections of the volatile compounds in organic solvents for external calibration purposes without the need to disassemble the PT/TD. The influence of the purge flow, purge time and volume of sample, on the purge efficiency of the PT system is studied. Desorption time and temperature are optimised for the TD mode of operation. Atomic absorption spectrometry (AAS) and flame photometric detection (FPD) have been used for the final determination of the volatile compounds. The figures of merit achieved with both detectors are reported.     

YinYang atom: a simple combined ab initio quantum mechanical molecular mechanical model

A simple interface is proposed for combined quantum mechanical (QM) molecular mechanical (MM) calculations for the systems where the QM and MM regions are connected through covalent bonds. Within this model, the atom that connects the two regions, called YinYang atom here, serves as an ordinary MM atom to other MM atoms and as a hydrogen-like atom to other QM atoms. Only one new empirical parameter is introduced to adjust the length of the connecting bond and is calibrated with the molecule propanol. This model is tested with the computation of equilibrium geometries and protonation energies for dozens of molecules. Special attention is paid on the influence of MM point charges on optimized geometry and protonation energy, and it is found that it is important to maintain local charge-neutrality in the MM region in order for the accurate calculation of the protonation and deprotonation energies. Overall the simple YinYang atom model yields comparable results to some other QM/MM models.     

Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born surface area methods. II. The accuracy of ranking poses generated from docking

In molecular docking, it is challenging to develop a scoring function that is accurate to conduct high-throughput screenings. Most scoring functions implemented in popular docking software packages were developed with many approximations for computational efficiency, which sacrifices the accuracy of prediction. With advanced technology and powerful computational hardware nowadays, it is feasible to use rigorous scoring functions, such as molecular mechanics/Poisson Boltzmann surface area (MM/PBSA) and molecular mechanics/generalized Born surface area (MM/GBSA) in molecular docking studies. Here, we systematically investigated the performance of MM/PBSA and MM/GBSA to identify the correct binding conformations and predict the binding free energies for 98 protein-ligand complexes. Comparison studies showed that MM/GBSA (69.4%) outperformed MM/PBSA (45.5%) and many popular scoring functions to identify the correct binding conformations. Moreover, we found that molecular dynamics simulations are necessary for some systems to identify the correct binding conformations. Based on our results, we proposed the guideline for MM/GBSA to predict the binding conformations. We then tested the performance of MM/GBSA and MM/PBSA to reproduce the binding free energies of the 98 protein-ligand complexes. The best prediction of MM/GBSA model with internal dielectric constant 2.0, produced a Spearman's correlation coefficient of 0.66, which is better than MM/PBSA (0.49) and almost all scoring functions used in molecular docking. In summary, MM/GBSA performs well for both binding pose predictions and binding free-energy estimations and is efficient to re-score the top-hit poses produced by other less-accurate scoring functions.     

Development of a Novel Acoustic Spectroscopy Method for Detection of Eggshell Cracks

Non-destructive testing (NDT) for eggshell faults is highly important for the egg industry, as cracked eggs account for around 3% of total production. The most commonly used method at present, candling, is labor intensive, while computer vision systems are expensive and complicated. In this paper, we present a simple, yet efficient, novel method for eggshell crack detection by acoustic spectroscopy. Altogether, 693 sound recordings were evaluated by different classification methods. The results show a cross-validated 2.1% total classification error, with only 0.87% false positive rate, which is the crucial metric for fresh eggs. Adapting the developed method to an industrial setting may lead to a reliable, fast and cost-effective detection method.