GROMACS: fast, flexible, and free

This article describes the software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the early 1990s. The software, written in ANSI C, originates from a parallel hardware project, and is well suited for parallelization on processor clusters. By careful optimization of neighbor searching and of inner loop performance, GROMACS is a very fast program for molecular dynamics simulation. It does not have a force field of its own, but is compatible with GROMOS, OPLS, AMBER, and ENCAD force fields. In addition, it can handle polarizable shell models and flexible constraints. The program is versatile, as force routines can be added by the user, tabulated functions can be specified, and analyses can be easily customized. Nonequilibrium dynamics and free energy determinations are incorporated. Interfaces with popular quantum-chemical packages (MOPAC, GAMES-UK, GAUSSIAN) are provided to perform mixed MM/QM simulations. The package includes about 100 utility and analysis programs. GROMACS is in the public domain and distributed (with source code and documentation) under the GNU General Public License. It is maintained by a group of developers from the Universities of Groningen, Uppsala, and Stockholm, and the Max Planck Institute for Polymer Research in Mainz. Its Web site is http://www.gromacs.org.     

Relativistic all-electron configuration interaction calculations on the gold atom

We present the results of relativistic and non-relativistic self-consistent field and configuration interaction calculations for the gold atom, using the spin-free no-pair Hamiltonian in a basis set expansion. A new basis set for the gold atom is discussed and its results in relativistic and non-relativistic self-consistent field calculations are compared to those of numerical Dirac-Hartree-Focic and Hartree-Fock calculations, respectively. Excitation energies, electron affinities and ionization potentials were calculated using a multi-reference configuration interaction technique and are in reasonable agreement with experiment in the relativistic case.     

Purification and characterization of a laccase from the white-rot fungus Trametes multicolor

The wood-degrading fungus Trametes multicolor secretes several laccase isoforms when grown on a simple medium containing copper in the millimolar range for stimulating laccase synthesis. The main isoenzyme laccase II was purified to apparent homogeneity from the culture supernatant by using anion-exchange chromatography and gel filtration. Laccase II is a monomeric glycoprotein with a molecular mass of 63 kDa as determined by sodium dodecylsulfate polyacrylamide gel electrophoresis, contains 18% glycosylation, and has a pI of 3.0. It oxidizes a variety of phenolic substrates as well as ferrocyanide and iodide. The pH optimum depends on the substrate employed and shows a bell-shaped pH activity profile with an optimum of 4.0 to 5.0 for the phenolic substrates, while the nonphenolic substrates ferrocyanide and 2,2′-azino-bis(3-ethylbenzthiazoline-6-sulfonate) show a monotonic pH profile with a rate decreasing with increasing pH.     

Zur Bestimmung der gesamten und freien schwefligen S?ure im Wein

Zusammenfassung Ein Vergleich der Methoden von Weinmann u. Deibner zur Bestimmung der gesamten schwefligen Säure zeigte, daß die letzte Methode zu exakteren Werten führt,vor allem dadurch bedingt, daß das überdestillierte Schwefeldioxyd in einer sauren gekühlten Vorlage aufgefangen wird. Ein Nachteil der Methode ist, daß bei der Titration der Vorlage mit Jodlösung der p_H-Wert mehrfach geändert werden muß. Es gelang uns, diesen Mangel ohne Einbuße an Analysengenauigkeit dadurch zu beseitigen, daß wir als Auffanglösung ein Puffergemisch (p_H 3,5) benutzen und nicht in saurem, sondern in schwach alkalischem Milieu mit Jodlösung titrieren. In dieser Form kann das Verfahren zur Bestimmung der gesamten schwefligen Säure im Wein empfohlen werden.Zur genauen Bestimmung der freien schwefligen Säure arbeiteten wir ein polarographisches Verfahren aus, bei dem im Gegensatz zur jodometrischen Methode die koordinativ gebundene schweflige Säure nicht miterfaßt wird. Der verhältnismäßig große apparative Aufwand bei der Polarographie spricht jedoch gegen die Anwendung dieses Verfahrens in der routinemäßigen Weinanalyse. Es wird deshalb eine vereinfachte, aber recht genaue jodometrische Methode zur Bestimmung der freien schwefligen Säure vorgestellt, die geeignet ist, Aufnahme in die neue Allgemeine Verwaltungsvorschrift für die Untersuchung von Wein und ähnlichen alkoholischen Erzeugnissen sowie von Fruchtsäften zu finden, die an die Stelle der alten Amtlichen Anweisung getreten ist.Für die Untersuchungen wurden Mittel des Bundesernährungsministeriums zur Verfügung gestellt, wofür auch an dieser Stelle bestens gedankt sei.Die Arbeit stellt einen Ausschnitt dar aus der Diplomarbeit von D. Hess: Beitrag zur Bestimmung der schwefligen Säure im Wein (Universität Frankfurt/M. 1957) und der Dissertation von D. Hess: Über den Einfluß von schwefliger Säure und l-Ascorbinsäure bei der Weinbereitung (Frankfurt/M. 1960).     

Metabolism of levamisole and kinetics of levamisole and aminorex in urine by means of LC-QTOF-HRMS and LC-QqQ-MS

The antihelminthic drug Levamisole can enhance cocaine effects by conversion into the amphetamine-like drug aminorex. We describe an LC-MS method for the determination of levamisole and its metabolite aminorex in human urine. Selectivity is given, calibration curves were linear within the calibration range 2.5–250 ng/mL; limits of the method were LoD 0.51 ng/mL, LoQ 1.02 ng/mL for levamisole and LoD 0.65 ng/mL, LoQ 0.76 ng/mL for aminorex. Precision data was in accordance with the guidelines (intraday precision for aminorex ranged between 5.75 and 11.0 % for levamisole between 8.36 and 10.9 %; interday precision for levamisole 10.9–16.9 % and for aminorex 7.64–12.7 %; accuracy data for levamisole ?1.96 to –14.3 % and for aminorex?11.9 to–18.5 %). The validated method was successfully applied to study the urinary excretion of levamisole after the administration of 100 mg of levamisole orally. Levamisole and aminorex could be detected in post-administration urine samples. Levamisole could be detected up to 39 h after ingestion, while aminorex was detectable up to 54 h. Maximum aminorex concentrations were 45 ng/mL urine. Further metabolites of levamisole after oral ingestion by means of liquid chromatography hybrid quadrupole time-of-flight high-resolution mass spectrometry (LC-QTOF-HRMS) were identified. Only 0.5 % of the ingested drug was quantified as unchanged levamisole in urine. Besides aminorex, five isomers of aminorex and 4 hydroxy-metabolites of aminorex or its isomers were found. Furthermore, levamisole is also hydroxylated and eliminated free or conjugated with sulfate or glucuronide into urine.     

Reduced field-of-view diffusion-weighted imaging of the brain at 7 T

Ventral and rostral regions of the brain are of emerging importance for the MRI characterization of early dementia, traumatic brain injury and epilepsy. Unfortunately, standard single-shot echo planar diffusion-weighted imaging of these regions at high fields is contaminated by severe imaging artifacts in the vicinity of air–tissue interfaces. To mitigate these artifacts and improve visualization of the temporal and frontal lobes at 7 T, we applied a reduced field-of-view strategy, enabled by outer volume suppression (OVS) with novel quadratic phase radiofrequency (RF) pulses, combined with partial Fourier and parallel imaging methods. The new acquisition greatly reduced the level of artifacts in six human subjects (including four patients with early symptoms of dementia).     

The Reactions of 2,2,2-Trichloro-1-phenylethanone with O,C and S Nucleophiles

The reactions of 2,2,2-trichloro-1-phenylethanone with various oxygen, carbon and sulfur nucleophiles were investigated with a view of widening the use of trichloroethanones as acylating agents.     

Synthesis and thermal properties of diurethanes containing various mesogenic units

Abstract

Five homologous series of diurethanes containing mesogenic moieties were synthesized by addition reactions of ω-alkenols to aromatic diisocyanates. The thermal behaviour of the compounds was studied by differential scanning calorimetry and on the hot stage of a polarizing microscope. Thermotropic liquid crystal behaviour was found for the diurethanes having a central core of more than two aromatic rings. Smectic C mesophases were observed for the derivatives of 4,4″-p-terphenylene and nematic mesophases for the diurethanes containing a di(4-phenylene)terephthalate unit. The compounds of both series possess high transition temperatures and narrow mesomorphic ranges.     

Approximate chemical analysis of volcanic glasses using Raman spectroscopy

The effect of chemical composition on the Raman spectra of a series of natural calcalkaline silicate glasses has been quantified by performing electron microprobe analyses and obtaining Raman spectra on glassy filaments (~450 µm) derived from a magma mingling experiment. The results provide a robust compositionally‐dependent database for the Raman spectra of natural silicate glasses along the calcalkaline series. An empirical model based on both the acquired Raman spectra and an ideal mixing equation between calcalkaline basaltic and rhyolitic end‐members is constructed enabling the estimation of the chemical composition and degree of polymerization of silicate glasses using Raman spectra. The model is relatively insensitive to acquisition conditions and has been validated using the MPI‐DING geochemical standard glasses 1 as well as further samples. The methods and model developed here offer several advantages compared with other analytical and spectroscopic methods such as infrared spectroscopy, X‐ray fluorescence spectroscopy, electron and ion microprobe analyses, inasmuch as Raman spectroscopy can be performed with a high spatial resolution (1 µm²) without the need for any sample preparation as a nondestructive technique. This study represents an advance in efforts to provide the first database of Raman spectra for natural silicate glasses and yields a new approach for the treatment of Raman spectra, which allows us to extract approximate information about the chemical composition of natural silicate glasses using Raman spectroscopy. We anticipate its application in handheld in situ terrestrial field studies of silicate glasses under extreme conditions (e.g. extraterrestrial and submarine environments). © 2015 The Authors Journal of Raman Spectroscopy Published by John Wiley & Sons Ltd