Structure and dynamics of liquid water with different long-range interaction truncation and temperature control methods in molecular dynamics simulations

We have used molecular dynamics simulations to study the physical properties of modified TIP3P water model included in the CHARMM program, using four different methods-the Ewald summation technique, and three different spherical truncation methods-for the treatment of the long-range interactions. Both the structure and dynamics of the liquid water model were affected by the methods used to truncate the long-range interactions. For some of the methods artificial structuring of the model liquid was observed around the cutoff radius. The model liquid properties were also affected by the commonly applied temperature control methods. Four different methods for controlling the temperature of the system were studied, and the effects of these methods on the bulk properties for liquid water were analyzed. The system size was also found to change the dynamics of the model liquid water. Two control simulations with the SPC/E water model were carried out. The self-diffusion coefficient (D), the radial distribution function (g(OO)), the distance dependent Kirkwood G-factor [G(k)(r)] and the intermolecular potential energy (E(pot)) were determined from the different trajectories and compared with the experimental data.     

Multi‐state multi‐reference Møller–Plesset second‐order perturbation theory for molecular calculations

This work presents multi‐state multi‐reference Møller–Plesset second‐order perturbation theory as a variant of multi‐reference perturbation theory to treat electron correlation in molecules. An effective Hamiltonian is constructed from the first‐order wave operator to treat several strongly interacting electronic states simultaneously. The wave operator is obtained by solving the generalized Bloch equation within the first‐order interaction space using a multi‐partitioning of the Hamiltonian based on multi‐reference Møller–Plesset second‐order perturbation theory. The corresponding zeroth‐order Hamiltonians are nondiagonal. To reduce the computational effort that arises from the nondiagonal generalized Fock operator, a selection procedure is used that divides the configurations of the first‐order interaction space into two sets based on the strength of the interaction with the reference space. In the weaker interacting set, only the projected diagonal part of the zeroth‐order Hamiltonian is taken into account. The justification of the approach is demonstrated in two examples: the mixing of valence Rydberg states in ethylene, and the avoided crossing of neutral and ionic potential curves in LiF. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Suppressing one‐bond homonuclear 13C,13C scalar couplings in the J‐HMBC NMR experiment: application to 13C site‐specifically labeled oligosaccharides

Site‐specific ¹³C isotope labeling is a useful approach that allows for the measurement of homonuclear ¹³C,¹³C coupling constants. For three site‐specifically labeled oligosaccharides, it is demonstrated that using the J‐HMBC experiment for measuring heteronuclear long‐range coupling constants is problematical for the carbons adjacent to the spin label. By incorporating either a selective inversion pulse or a constant‐time element in the pulse sequence, the interference from one‐bond ¹³C,¹³C scalar couplings is suppressed, allowing the coupling constants of interest to be measured without complications. Experimental spectra are compared with spectra of a nonlabeled compound as well as with simulated spectra. The work extends the use of the J‐HMBC experiments to site‐specifically labeled molecules, thereby increasing the number of coupling constants that can be obtained from a single preparation of a molecule. Copyright © 2014 John Wiley & Sons, Ltd.     

Trifluoroethylxanthate as an Analytical Reagent: AAS of Zinc,Antimony and Lead After Coprecipitation of Their Trifluoroethylxanthates onto Microcyrstalline Naphthalene

Abstract

A sensitive method has been developed for the direct atomic absorption spectrometric determination of zinc, antimony and lead after coprecipitation of their trifluoroethylxanthates onto microcrystalline naphthalene. The metal xanthates are quantitatively coprecipitated over the pH ranges: Zn, 5.9–8.4; Sb, 4.0–6.0 and Pb, 4.0–11.0. The solid mass consisting of the metal complex and naphthalene is dissolved in DMF. This solution is aspirated into an air-acetylene flame at 213.9, 217.6 and 217.0nm for Zn, Sb and Pb, respectively. Beer's law is obeyed in the concentration range 2–50, 3–90 and 5–60 μg of Zn, Sb and Pb, respectively in 10ml of the final DMF solution. RSDs are at the ± (0.5–0.6)% level (n=10). The concentration for 1% absorption is 0.019, 0.035 and 0.060μg/ml for Zn, Sb and Pb, respectively. The method is suitable for the preconcentration of the metals from a larger volume of the aqueous phase, and has been employed for their determination in standard reference materials. It may be employed for the simultaneous determination of Zn, Pb and Sb in a solution by pH control.     

A dissipation‐free numerical method to solve one‐dimensional hyperbolic flow equations

In this paper, a numerical method to capture the shock wave propagation in 1‐dimensional fluid flow problems with 0 numerical dissipation is presented. Instead of using a traditional discrete grid, the new numerical method is built on a range‐discrete grid, which is obtained by a direct subdivision of values around the shock area. The range discrete grid consists of 2 types: continuous points and shock points. Numerical solution is achieved by tracking characteristics and shocks for the movements of continuous and shock points, respectively. Shocks can be generated or eliminated when triggering entropy conditions in a marking step. The method is conservative and total variation diminishing. We apply this new method to several examples, including solving Burgers equation for aerodynamics, Buckley‐Leverett equation for fractional flow in porous media, and the classical traffic flow. The solutions were verified against analytical solutions under simple conditions. Comparisons with several other traditional methods showed that the new method achieves a higher accuracy in capturing the shock while using much less grid number. The new method can serve as a fast tool to assess the shock wave propagation in various flow problems with good accuracy.     

Identification and quantification of the antipsychotics risperidone,aripiprazole, pipamperone and their major metabolites in plasma using ultra‐high performance liquid chromatography–mass spectrometry

The antipsychotics risperidone, aripiprazole and pipamperone are frequently prescribed for the treatment in children with autism. The aim of this study was to validate an ultra‐high performance liquid chromatography–mass spectrometry method for the quantification of these antipsychotics in plasma. An ultra‐high performance liquid chromatography–mass spectrometry assay was developed for the determination of the drugs and metabolites. Gradient elution was performed on a reversed‐phase column with a mobile phase consisting of ammonium acetate, formic acid in methanol or in Milli‐Q ultrapure water at a flow rate of 0.5 mL/min. The method was validated according to the US Food and Drug Administration guidelines. The analytes were found to be stable enough after reconstitution and injection of only 5 μL improved the accuracy and precision in combination with the internal standard. Calibration curves of all five analytes were linear. All analytes were stable for at least 72 h in the autosampler and the high quality control of 9‐OH‐risperidone was stable for 48 h. The method allows quantification of all analytes. The advantage of this method is the combination of a minimal injection volume, a short run‐time, an easy sample preparation method and the ability to quantify all analytes in one run. Copyright © 2015 John Wiley & Sons, Ltd.     

A dynamic process interpretation of the sparse ERGM reference model

Exponential family random graph models (ERGMs) can be understood in terms of a set of structural biases that act on an underlying reference distribution. This distribution determines many aspects of the behavior and interpretation of the ERGM families incorporating it. One important innovation in this area has been the development of an ERGM reference model that produces realistic behavior when generalized to sparse networks of varying sizes. Here, we show that this model can be derived from a latent dynamic process in which tie formation takes place within small local settings between which individuals move. This derivation provides one possible micro-process interpretation of the sparse ERGM reference model and sheds light on the conditions under which constant mean degree scaling can emerge.     

A rapid and simple HPTLC assay for therapeutic drug monitoring of capecitabine in colorectal cancer patients

Capecitabine is a prodrug of 5‐flurouracil, employed as a broad spectrum chemotherapeutic agent. It is also used as monotherapy or a combination chemotherapy agent for the treatment of colorectal cancer. Capecitabine is administered in combination with oxaliplatin and hence it is essential to determine that co‐administration does not affect its metabolism. To determine the plasma concentration of capecitabine a simple HPTLC method was developed and validated. Blood samples from 12 patients with colorectal cancer were collected and analyzed by the HPTLC method with a reference internal standard. Out of these 12 patients, six were treated with capecitabine monotherapy and another six were treated with capecitabine + oxaliplatin combination therapy. The results of analysis indicated that there was no significant drug–drug interaction and the co‐administration of oxaliplatin did not affect the metabolism of capecitabine. This method is sensitive, robust and specific and allows analysis of multiple samples simultaneously, making it suitable for therapeutic drug monitoring of capecitabine.     

A simple,rapid and reliable liquid chromatography–mass spectrometry method for determination of methotrexate in human plasma and its application to therapeutic drug monitoring

A simple, rapid and reliable liquid chromatography–electrospray ionization tandem mass spectrometry method was established and validated for the determination of methotrexate in human plasma. After a straightforward protein precipitation by acetonitrile–water (70:30, v/v), methotrexate (MTX) and p‐aminoacetophenone (used as internal standard, IS) were separated on a Column C₁₈ column (50 × 2.1 mm, 3 µm; Column Technology, Fremont, CA, USA) using a gradient elution with mobile phase of acetonitrile and 0.03% acetic acid aqueous solution at a flow rate of 0.5 mL/min. The total chromatographic runtime was 5 min for each injection. Quantification detection was performed in a triple‐quadruple tandem mass spectrometer under positive mode monitoring the following mass transitions: m/z 455.3 → 308.3 for MTX and m/z 136.1 → 94.4 for IS. The calibration curve was linear over the range of 0.05–25.0 µmol/L with a lower limit of quantification of 0.05 µmol/L. The intra‐ and interday precisions were <5.2%, the accuracy varied from ?4.1 to 4.5%. The recovery was >94%. The LC‐MS/MS method showed an excellent agreement with the existing HPLC‐UV method using Passing–Bablok regression and Bland–Altman difference plot analysis. The validated LC‐MS/MS can be successfully applied to the routine therapeutic drug monitoring of MTX in clinical laboratories. Copyright © 2015 John Wiley & Sons, Ltd.