Enabling grand‐canonical Monte Carlo: Extending the flexibility of GROMACS through the GromPy python interface module

We report on a python interface to the GROMACS molecular simulation package, GromPy (available at https://github.com/GromPy ). This application programming interface (API) uses the ctypes python module that allows function calls to shared libraries, for example, written in C. To the best of our knowledge, this is the first reported interface to the GROMACS library that uses direct library calls. GromPy can be used for extending the current GROMACS simulation and analysis modes. In this work, we demonstrate that the interface enables hybrid Monte‐Carlo/molecular dynamics (MD) simulations in the grand‐canonical ensemble, a simulation mode that is currently not implemented in GROMACS. For this application, the interplay between GromPy and GROMACS requires only minor modifications of the GROMACS source code, not affecting the operation, efficiency, and performance of the GROMACS applications. We validate the grand‐canonical application against MD in the canonical ensemble by comparison of equations of state. The results of the grand‐canonical simulations are in complete agreement with MD in the canonical ensemble. The python overhead of the grand‐canonical scheme is only minimal. © 2012 Wiley Periodicals, Inc.     

Estimation of crude oil grade using time-resolved fluorescence spectra

Time-resolved fluorescence (TRF) spectra of six crude oils from the eastern province of Saudi Arabia were excited using a pulsed laser radiation at 250 nm and measured at specific time gates (TG) within the leading and trailing edges of the laser temporal pulse. The spectra showed the presence of a shoulder near 380 nm that systematically decreased in intensity from high-grade to low-grade crudes, and also from earlier to later TGs. The intensities of these shoulders are shown to be useful in estimating the grades of crude oils, particularly when the TRF spectra are measured at TGs within the leading edge of the laser temporal pulse. Contour diagrams depicting the shapes of the TRF spectra as function of TG (within the leading and trailing edges) are also presented to serve as true fingerprints of the crudes.     

Measuring Bismuth Oxide Particle Size and Morphology in Film-Coated Tablets

The assessment of active pharmaceutical ingredient (API) particle size and morphology is of great importance for the pharmaceutical industry since it is expected to significantly affect physicochemical properties. However, very few methods are published for the determination of API morphology and particle size of film-coated (FC) tablets. In the current study we provide a methodology for the measurement of API particle size and morphology which could be applied in several final products. Bismuth Oxide 120 mg FC Tabs were used for our method development, which contain bismuth oxide (as tripotassium dicitratobismuthate (bismuth subcitrate)) as the active substance. The sample preparation consists of partial excipient dissolution in different solvents. Following this procedure, the API particles were successfully extracted from the granules. Particle size and morphology identification in Bismuth Oxide 120 mg FC Tabs was conducted using micro-Raman mapping spectroscopy and ImageJ software. The proposed methodology was repeated for the raw API material and against a reference listed drug (RLD) for comparative purposes. The API particle size was found to have decreased compared to the raw API, while the API morphology was also affected from the formulation manufacturing process. Comparison with the RLD product also revealed differences, mainly in the API particle size and secondarily in the crystal morphology.     

Green Solvents for Eco-Friendly Synthesis of Dimethindene: A Forward-Looking Approach

Dimethindene is a selective histamine H₁ antagonist and is commercially available as a racemate. Upon analyzing the synthetic pathways currently available for the industrial preparation of dimethindene, we set up a sustainable approach for the synthesis of this drug, switching from petroleum-based volatile organic compounds (VOCs) to eco-friendly solvents, such as 2-methyltetrahydrofuran (2-MeTHF) and cyclopentyl methyl ether (CPME) belonging to classes 3 and 2, respectively. Beyond decreasing the environmental impact of the synthesis (E-factor: 24.1–54.9 with VOCs; 12.2–22.1 with 2-MeTHF or CPME), this switch also improved the overall yield of the process (from 10% with VOCs to 21–22% with 2-MeTHF or CPME) and remarkably simplified the manual operations, working under milder conditions. Typical metrics applied at the first and second pass, according to the CHEM21 metrics toolkit, were also calculated for the whole synthetic procedure of dimethindene, and the results were compared with those of the classical procedure.     

Reviews on recent trends in chromatography/mass spectrometry coupling. Part IV. Reasons why supercritical fluid chromatography is not so easily coupled with mass spectrometry as originally assessed

Summary When SFC was rediscovered in the early 1980s, it was frequently estimated that a strong driving force to its development would be the ease of devising a simple SFC/MS interface. This was believed to be easily achieved if analytical conditions were limited to capillary SFC columns as a general separation tool, and to the choice of neat CO₂ as the unique supercritical fluid. The low flow rate of mobile phase delivered by capillary columns was easy to accommodate by the vacuum equipment of standard mass spectrometers, and the specific physical properties of CO₂ made possible solute ionization by different ion-molecule reactions, especially charge exchange ionization. This approach has lived up to all of its promises. The major causes of the observed mismatch are the large variations of the MS source pressure as a result of the CO₂ pressure gradient at the SFC column inlet, the low sensitivity of charge exchange ionization at these high MS source pressures, and the inability to handle polar and nonvolatile molecules. Adaptation of LC/MS interfaces, such as the thermospray interface or the particle beam interface, to SFC/MS conditions was a step forward, but these devices have their own limitations. Alternative methods to direct SFC/MS coupling have been investigated recently. They are based on the use of packed columns rather than capillaries, and on solute ionization at atmospheric pressure rather than under a vacuum, by means of either gas-phase corona discharge ionization or liquidphase electrospray ionization. These new developments may revive research into the design of reproducible and sensitive SFC/MS systems where the number of recent studies is still low compared with other chromatography/mass spectrometry coupling studies.See [1] for part III     

Atmospheric pressure ionization–tandem mass spectrometry of the phenicol drug family

In this work, the mass spectrometry behaviour of the veterinary drug family of phenicols, including chloramphenicol (CAP) and its related compounds thiamphenicol (TAP), florfenicol (FF) and FF amine (FFA), was studied. Several atmospheric pressure ionization sources, electrospray (ESI), atmospheric pressure chemical ionization and atmospheric pressure photoionization were compared. In all atmospheric pressure ionization sources, CAP, TAP and FF were ionized in both positive and negative modes; while for the metabolite FFA, only positive ionization was possible. In general, in positive mode, [M + H]⁺ dominated the mass spectrum for FFA, while the other compounds, CAP, TAP and FF, with lower proton affinity showed intense adducts with species present in the mobile phase. In negative mode, ESI and atmospheric pressure photoionization showed the deprotonated molecule [M–H]^?, while atmospheric pressure chemical ionization provided the radical molecular ion by electron capture. All these ions were characterized by tandem mass spectrometry using the combined information obtained by multistage mass spectrometry and high‐resolution mass spectrometry in a quadrupole‐Orbitrap instrument. In general, the fragmentation occurred via cyclization and losses or fragmentation of the N‐(alkyl)acetamide group, and common fragmentation pathways were established for this family of compounds. A new chemical structure for the product ion at m/z 257 for CAP, on the basis of the MS³ and MS⁴ spectra is proposed. Thermally assisted ESI and selected reaction monitoring are proposed for the determination of these compounds by ultra high‐performance liquid chromatography coupled to tandem mass spectrometry, achieving instrumental detection limits down to 0.1 pg. Copyright © 2013 John Wiley & Sons, Ltd.     

Chromatographic-based methods for pesticide determination in honey: An overview

Nowadays the control of pesticides in honey is an issue of primary health importance as consequence of the increasing content of these chemicals in the aforementioned matrix. This poisoning has led to the worldwide increasing loss of bees since 1995. From Europe to Canada, scientist, beekeepers and chemical companies disagree about the reasons that have led to colony losses higher than 50% in some areas. This problem has become a public health issue due to the high honey worldwide consumption. The presence of pesticides in honey has been directly related to bees’ mortality by some researchers through pesticide presence in (1) pollen, (2) honeycomb walls, (3) own bees and (4) honey. In this work we describe the actual state-of-the-art for pesticides determination in honey along with a review in this subject focused on sample treatments and instrumentation. Finally, future trends are also commented.     

Sample preparation methods for subsequent determination of metals and non-metals in crude oil—A review

In this review sample preparation strategies used for crude oil digestion in last ten years are discussed focusing on further metals and non-metals determination. One of the main challenges of proposed methods has been to overcome the difficulty to bring crude oil samples into solution, which should be compatible with analytical techniques used for element determination. On this aspect, this review summarizes the sample preparation methods for metals and non metals determination in crude oil including those based on wet digestion, combustion, emulsification, extraction, sample dilution with organic solvents, among others. Conventional methods related to wet digestion with concentrated acids or combustion are also covered, with special emphasis to closed systems. Trends in sample digestion, such as microwave-assisted digestion using diluted acids combined with high-efficiency decomposition systems are discussed. On the other hand, strategies based on sample dilution in organic solvents and procedures recommended for speciation analysis are reported as well as the use of direct analysis in view of the recent importance for crude oil field. A compilation concerning sample preparation for crude oil provided by official methods as well as certified reference materials available for accuracy evaluation is also presented and discussed.     

A 21st century technique for food control: Electronic noses

This work examines the main features of modern electronic noses (e-noses) and their most important applications in food control in this new century. The three components of an electronic nose (sample handling system, detection system, and data processing system) are described. Special attention is devoted to the promising mass spectrometry based e-noses, due to their advantages over the more classical gas sensors. Applications described include process monitoring, shelf-life investigation, freshness evaluation, authenticity assessment, as well as other general aspects of the utilization of electronic noses in food control. Finally, some interesting remarks concerning the strengths and weaknesses of electronic noses in food control are also mentioned.