A new approximate method for the stochastic simulation of chemical systems: the representative reaction approach

We have developed two new approximate methods for stochastically simulating chemical systems. The methods are based on the idea of representing all the reactions in the chemical system by a single reaction, i.e., by the “representative reaction approach” (RRA). Discussed in the article are the concepts underlying the new methods along with flowchart with all the steps required for their implementation. It is shown that the two RRA methods {with the reaction as the representative reaction (RR)} perform creditably with regard to accuracy and computational efficiency, in comparison to the exact stochastic simulation algorithm (SSA) developed by Gillespie and are able to successfully reproduce at least the first two moments of the probability distribution of each species in the systems studied. As such, the RRA methods represent a promising new approach for stochastically simulating chemical systems. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2012     

Thermal rate constant for the C(3P) + OH(X2Π) → CO(X1Σ) + H(2S) reaction using stochastic energy grained master equation method

In the present work, the kinetic mechanism of the reaction is studied. The rate constants were determined using the Master Equation Solver for Multi-Energy Well Reactions (MESMER). The master equation modeling was also employed to examine the pressure dependence for each pathway involved. The theoretical analysis shows that the overall rate coefficient is practically independent of pressure up to 100 Torr for the temperature range 125-500 K. The unusual dependence of the overall rate constant with temperature was fit with the d-Arrhenius expression , where cm³molecule⁻¹s⁻¹, , and  kJ·mol⁻¹, for 125⩽ T ⩽ 500 K. The thermal rate constant results are in relatively good agreement with other theoretical studies.     

Insights into the Kramers’ flux‐over‐population rate for chemical reactions in liquid phases through the matrix transport equation

Kramers’ equation models a chemical reaction as a Brownian particle diffusing over a potential barrier under the influence of medium viscosity. In the case of high viscosity, the equation reduces to a simpler Smoluchowski equation. In this report, we have contrived an equivalent matrix‐transport equation that relates the ordered pair (activity, flux) of the output (activated complex) to that of the input (reactant). With an initial condition of the Dirac delta type placed at the location of the reactant, and a reflecting boundary condition set on the reactant state, and an absorbing boundary condition on the activated complex state, we are able to prove the equality relation between the mean first passage time, , for the diffusion and the inverse of the rate constant, k^?1, for the reaction counterpart. We have also derived , where λ_i is the ith eigenvalue of the Smoluchowski differential operator stipulated with the above‐mentioned boundary conditions. We have also deduced that, in the long time limit, the number of particles remaining inside the diffusion domain decays exponentially with a relaxation time just the same as the concentration of the reactant does for a first‐order reaction system.     

A fast method for the measurement of diffusion coefficients: one‐dimensional DOSY

A new experiment for the single‐scan measurement of diffusion coefficients is presented. The principle is to introduce a spatial variation in the parameters of a conventional pulse sequence, so that all of the scans required to determine some physical parameter can be recorded simultaneously from different parts of the sample. The spectrum is acquired in the presence of a weak read gradient so that the resulting lineshapes contain the information required. The pulse sequence is described in detail and demonstrated on a sample containing three components; its advantages and limitations are discussed in relation to those of existing techniques. For uncrowded spectra with high signal‐to‐noise ratio, this experiment provides an order of magnitude reduction in experiment time compared with conventional methods and is likely to be of most benefit where samples are changing rapidly with time or where a long period of polarization, which may be difficult to reproduce accurately, prohibits the use of multiple‐scan techniques. Copyright © 2003 John Wiley & Sons, Ltd.     

High‐performance liquid chromatography with diode‐array detection cotinine method adapted for the assessment of tobacco smoke exposure

Smoking is considered to be one of the main risk factors for cancer and other diseases and is the second leading cause of death worldwide. As the anti‐tobacco legislation implemented in Europe has reduced secondhand smoke exposure levels, analytical methods must be adapted to these new levels. Recent research has demonstrated that cotinine is the best overall discriminator when biomarkers are used to determine whether a person has ongoing exposure to tobacco smoke. This work proposes a sensitive, simple and low‐cost method based on solid‐phase extraction and liquid chromatography with diode array detection for the assessment of tobacco smoke exposure by cotinine determination in urine. The analytical procedure is simple and fast (20 min) when compared to other similar methods existing in the literature, and it is cheaper than the mass spectrometry techniques usually used to quantify levels in nonsmokers. We obtained a quantification limit of 12.30 μg/L and a recovery of over 90%. The linearity ranges used were 12–250 and 250–4000 μg/L. The method was successfully used to determine cotinine in urine samples collected from different volunteers and is clearly an alternative routine method that allows active and passive smokers to be distinguished.     

High‐order symplectic integration in quasi‐classical trajectory simulation: Case study for O(1D) + H2

Classical trajectory calculations for the O(¹D) + H₂ reaction system are employed to assess the effectiveness of the symplectic integrators. The sixth‐order symplectic integrator has been found to be the most suitable method for the quasi‐classical trajectory calculation of a long‐lived complex‐forming reaction system. In comparison with the traditional fourth‐order Runge–Kutta initialized fourth‐order Admas–Moulton–Hamming predictor‐corrector integrator (RK4‐AMH4), the sixth‐order symplectic integrator is six times less computationally expensive and exhibits better energy conservation. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

High‐performance liquid chromatography tandem mass spectrometry method for the determination of 2CC‐NBOMe and 25I‐NBOMe in human serum

2CC‐NBOMe {4‐chloro‐2,5‐dimethoxyphenethyl‐N‐[(2‐methoxyphenyl) methyl] ethanamine} and 25I‐NBOMe {2‐(4‐iodo‐2,5‐dimethoxyphenyl)‐N‐[(2‐methoxyphenyl) methyl] ethanamine} are of a class of N‐benzyl phenethylamine derivatives whose synthesis was first reported in the scientific literature in 2011. Recent reports from ‘personal drug experience websites’ and in the popular press indicate these drugs are the latest in a series of designer ‘Bath Salt’ drugs of abuse. The presented high‐performance liquid chromatography triple quadrupole mass spectrometry (HPLC/MS/MS) method was developed for the detection and quantification of 2CC‐NBOMe and 25I‐NBOMe in serum of intoxicated emergency department patients. The assay applies 2‐?(2,?5‐?dimethoxyphenyl)‐?N‐?(2‐?methoxybenzyl) ethanamine (25H‐NBOMe) as the internal standard. Samples were extracted using solid‐phase extraction columns. The chromatographic separation was performed on a Luna 3 µ C₈(2) 100 Å, 100 × 2.0 mm, column. Detection was accomplished by multiple‐reaction monitoring via an electrospray ionization source operating in the positive ionization mode. The calibration curves were linear over the investigated concentration range, 30–2000 pg/mL, with a lower limit of detection of 10 pg/mL for both 2CC‐NBOMe and 25I‐NBOMe. The method proved suitable for serum clinical toxicology testing. Two severely intoxicated emergency department patients were determined to have serum concentrations of 250 and 2780 pg/mL of 25I‐NBOMe using the presented method. Copyright © 2013 John Wiley & Sons, Ltd.     

Titanium Dioxide‐Grafted Copper Complexes: High‐Performance Electrocatalysts for the Oxygen Reduction Reaction in Alkaline Media

The sluggish kinetics of the oxygen reduction reaction (ORR) at the cathodes of fuel cells significantly hampers fuel cell performance. Therefore, the development of high‐performance, non‐precious‐metal catalysts as alternatives to noble metal Pt‐based ORR electrocatalysts is highly desirable for the large‐scale commercialization of fuel cells. TiO₂‐grafted copper complexes deposited on multiwalled carbon nanotubes (CNTs) form stable and efficient electrocatalysts for the ORR. The optimized catalyst composite CNTs@TiO₂–ZA–[Cu(phen)(BTC)] shows surprisingly high selectivity for the 4 e^? reduction of O₂ to water (approximately 97 %) in alkaline solution with an onset potential of 0.988 V vs. RHE, and demonstrates superior stability and excellent tolerance for the methanol crossover effect in comparison to a commercial Pt/C catalyst. The copper complexes were grafted onto the surface of TiO₂ through coordination of an imidazole‐containing ligand, zoledronic acid (ZA), which binds to TiO₂ through its bis‐phosphoric acid anchoring group. Rational optimization of the copper catalyst’s ORR performance was achieved by using an electron‐deficient ligand, 5‐nitro‐1,10‐phenanthroline (phen), and bridging benzene‐1,3,5‐tricarboxylate (BTC). This facile approach to the assembly of copper catalysts on TiO₂ with rationally tuned ORR activity will have significant implications for the development of high‐performance, non‐precious‐metal ORR catalysts.     

High‐throughput ultra high performance liquid chromatography coupled to quadrupole time‐of‐flight mass spectrometry method for the rapid analysis and characterization of multiple constituents of Radix Polygalae

Radix Polygalae, the dried roots of Polygala tenuifolia and P. sibirica , is one of the most well‐known traditional Chinese medicinal plants. It is an important medicinal plant that has been used as a sedative and to improve memory for a number of years in most of Asia. However, the in vivo constituents of the multiple constituents from Radix Polygalae remain unknown. In the current study, ultra high performance liquid chromatography coupled to quadrupole time‐of‐flight mass spectrometry and the MarkerLynx^TM software combined with multiple data processing approach were used to study the constituents in vitro and in vivo. A rapid and efficient method for the characterization of multiple constituents in the herbal medicine Radix Polygalae by ultra high performance liquid chromatography coupled to quadrupole time‐of‐flight mass spectrometry is described. In total, 35 compounds in the Radix Polygalae and 13 compounds absorbed into blood were characterized. Of the 35 compounds in vitro, ten were reported for first time. In the 13 compounds in vivo, six were prototype components and seven were metabolites were also elucidated for first time. This work narrowed the range of screening the potentially bioactive components and provided a basis for the quality control and mechanism of action.     

Computational method for the retarded potential in the real‐time simulation of quantum electrodynamics

We discuss the method to compute the integrals, which appear in the retarded potential term for a real‐time simulation based on quantum electrodynamics. We show that the oscillatory integrals over the infinite interval involved in them can be efficiently performed by the method developed by Ooura and Mori based on the double exponential formula. © 2016 Wiley Periodicals, Inc.     

High‐performance liquid chromatography with photodiode array detection and chemometrics method for the analysis of multiple components in the traditional Chinese medicine Shuanghuanglian oral liquid

Shuanghuanlian oral liquid, a traditional Chinese medicine preparation, is a mixture of three herbs (Flos Lonicerae, Radix Scutellariae and Fructus Forsythiae). In this study, the quantitative analysis of three main active compounds, chlorogenic acid, forsythin and baicalin in samples from different manufacturers was performed rapidly by high‐performance liquid chromatography coupled with photodiode array detection followed by Contour Projection coupled to stepwise regression treatment of the obtained three‐dimensional spectra in which the partial overlap between adjacent target components existed. The method was validated for linearity (R>0.9940), precision (RSD<1.25%), recovery (92.20–102.50%), limit of detection (0.01–0.02 μg/mL) and limit of quantification (0.03–0.07 μg/mL). The results indicated that the combination of the three‐dimensional spectra of traditional Chinese medicine and Contour Projection‐stepwise regression offered an accurate, simple, low‐cost and eco‐friendly way for the rapid quantitative analysis of Shuanghuanlian oral liquid samples.     

High‐performance liquid chromatography with diode array detection method for the simultaneous determination of seven selected phosphodiesterase‐5 inhibitors and serotonin reuptake inhibitors used as male sexual enhancers

This work presents a simple, sensitive and generic high‐performance liquid chromatography with diode array detection method for the simultaneous determination of seven drugs prescribed for the treatment of erectile dysfunction and premature ejaculation. Investigated drugs include the phosphodiesterase‐5 inhibitors: sildenafil, tadalafil, and vardenafil, in addition to the selective serotonin reuptake inhibitors: dapoxetine, duloxetine, fluoxetine, and paroxetine. The drugs were separated using a Waters C8 column (4.6 × 250 mm, 5 μm) with the mobile phase consisting of phosphate buffer pH 3, acetonitrile and methanol in the ratio 60:33:7. The flow rate was 1.2 mL/min, and quantification was based on measuring peak areas at 225 nm. Peaks were perfectly resolved with retention times 3.3, 3.9, 6.4, 7.5, 9.5, 10.7, and 13.4 min for vardenafil, sildenafil, paroxetine, duloxetine, dapoxetine, fluoxetine, and tadalafil, respectively. The developed method was validated with respect to system suitability, linearity, ranges, accuracy, precision, robustness, and limits of detection and quantification. The proposed method showed good linearity in the ranges 5–500, 2–200, 2–200, 3–300, 1.5–150, 2–200, and 2–200 μg/mL for sildenafil, tadalafil, vardenafil, dapoxetine, duloxetine fluoxetine, and paroxetine, respectively. The limits of detection were 0.18–0.38 μg/mL for the analyzed compounds. The applicability of the proposed method to real life situations was assessed through the analysis of commercial tablets, and satisfactory results were obtained.     

High‐performance liquid chromatographic column packings with different particle sizes: Chromatographic behavior for the quality analysis of HuanglianShangqing pill

The chromatographic separation of traditional Chinese medicines is still a highly challenging task in analytical science with respect to its hundreds and thousands of chemical compounds, while increase of separation efficiency can greatly improve the separation power of chromatographic column for traditional Chinese medicine. In this study, 13 bioactive components in HuanglianShangqing pill were selected as an index to optimize the separation conditions and evaluate the system suitability of three commercially available columns packed with 1.8, 3.5, and 5.0 μm particles. The chromatographic separations were obtained by the most appropriate Eclipse Plus C₁₈ column (100 × 2.1 mm, 3.5 μm) within 45 min using gradient elution with aqueous‐ammonium acetate (10 mmol/L, pH 5.0) and acetonitrile, at a flow rate of 0.3 mL/min and an operating temperature of 30°C. The quality of HuanglianShangqing pill was assessed through combining simultaneous quantification of 13 compounds with fingerprint analysis. For the qualitative analysis, mass spectrometry was used to confirm the 13 compounds. All the validation data conformed to the acceptable requirements. For the fingerprint analysis, 32 peaks were selected as the common peaks at 254 nm to evaluate the similarities among HuanglianShangqing pills obtained from ten manufacturers.     

Accurate reaction barrier heights of pericyclic reactions: Surprisingly large deviations for the CBS‐QB3 composite method and their consequences in DFT benchmark studies

Accurate barrier heights are obtained for the 26 pericyclic reactions in the BHPERI dataset by means of the high‐level Wn‐F12 thermochemical protocols. Very often, the complete basis set (CBS)‐type composite methods are used in similar situations, but herein it is shown that they in fact result in surprisingly large errors with root mean square deviations (RMSDs) of about 2.5 kcal mol^?1. In comparison, other composite methods, particularly G4‐type and estimated coupled cluster with singles, doubles, and quasiperturbative triple excitations [CCSD(T)/CBS] approaches, show deviations well below the chemical‐accuracy threshold of 1 kcal mol^?1. With the exception of SCS‐MP2 and the herein newly introduced MP3.5 approach, all other tested Møller‐Plesset perturbative procedures give poor performance with RMSDs of up to 8.0 kcal mol^?1. The finding that CBS‐type methods fail for barrier heights of these reactions is unexpected and it is particularly troublesome given that they are often used to obtain reference values for benchmark studies. Significant differences are identified in the interpretation and final ranking of density functional theory (DFT) methods when using the original CBS‐QB3 rather than the new Wn‐F12 reference values for BHPERI. In particular, it is observed that the more accurate Wn‐F12 benchmark results in lower statistical errors for those methods that are generally considered to be robust and accurate. Two examples are the PW6B95‐D3(BJ) hybrid‐meta‐general‐gradient approximation and the PWPB95‐D3(BJ) double‐hybrid functionals, which result in the lowest RMSDs of the entire DFT study (1.3 and 1.0 kcal mol^?1, respectively). These results indicate that CBS‐QB3 should be applied with caution in computational modeling and benchmark studies involving related systems. © 2015 Wiley Periodicals, Inc.     

Ultra‐performance liquid chromatography MS/MS method for the determination of parabens in compost from sewage sludge: Comparison of the efficiency of two extraction techniques

The efficiency of two extraction techniques—ultrasound‐assisted extraction and pressurized liquid extraction—are compared and evaluated in the determination of parabens in compost samples. The extraction parameters for each technique were accurately optimized. The selected compounds were detected and quantified using ultra‐performance LC MS/MS, operating in negative ESI and in SRM mode. The analytes were separated in less than 5 min. Ethylparaben (ring‐¹³C₆ labeled) was used as an internal standard. Two selective, sensitive, and accurate analytical methods were developed and validated. The LODs of the methods ranged from 3 to 7 ng/g and the LOQs from 10 to 23 ng/g, while inter‐ and intraday variability was under 6% in all cases. The methods were validated separately by using matrix‐matched calibration and recovery assays with spiked samples. Recovery rates ranged from 94.0 to 105.0%. Compost samples were taken from different composting plants. Although the statistical comparison demonstrated no statistically significant differences between the two extraction techniques, the method based on pressurized liquid extraction was more sensitive than the ultrasound extraction based method.