Monte Carlo structure simulations for aqueous 1,4-dioxane solutions

Monte Carlo simulations in the NpT ensembles have been performed for the structure exploration of aqueous 1,4-dioxane solutions. Three different systems with all-atom dioxane:TIP4P water molar compositions of 2:500 (code:D2), 8:465 (D8), and 17:425 (D17) modeled solutions of 0.22, 0.88, and 1.86 mol/dm3 concentrations, respectively, at T = 298 K and p = 1 atm. The calculated solution densities increase from 0.992 to 1.002 g/cm3 with increasing dioxane concentration and approach the experimentally determined densities within 1%. This close agreement was achieved by utilizing RESP charges fitted to the in-solution IEF-PCM/B3LYP/6-31G* electrostatic potential of dioxane taken in its chair conformation and recently developed C, H steric parameters for ethers for calculations with a 12-6-1 all-atom potential. Solution structure analyses pointed out that the dioxane molecules arrange in the solutions with favorable distances of 4-8 angstroms for the ring symmetry centers. Within this range not only pairs of rings but triangular triads and tetrads have also been observed with center-center distances <8 angstroms. For the D8 system, about 25% of the sampled configurations included such a triad. In the case of the D17 model, two simulations starting from different solution configuration predicted different degrees for the dioxane aggregation in aqueous solution. In the more aggregated structure 3-21 triads are consistently maintained and 1-2 tetrads are formed in 58% of the configurations. Each dioxane oxygen forms about one hydrogen bond, on average, to a water molecule in the 0.22-1.86 molar range. The most likely O(dioxane)...H(water) hydrogen bond distance is 1.75-1.80 angstroms compared to the optimal distance of 1.72 angstroms in the isolated dimer. The optimal dioxane-water interaction energy of -5.65 kcal/mol indicates a remarkable hydrogen-bond acceptor character for dioxane.     

OPLC Comparison of Methods for Aqueous Extraction of Sennae folium and Tiliae flos Plant Samples

JPC – Journal of Planar Chromatography – Modern TLC - A new, simplified open-vessel microwave extraction (OVME) method has been used to prepare aqueous extracts of Sennae folium and...     

Fully On-Line Hyphenation of an Experimental OPLC Separation Unit with Diode-Array Detection and Mass-Spectrometry (OPLC-DAD-MS) for Analysis of Xanthine Compounds

JPC – Journal of Planar Chromatography – Modern TLC - The newly developed experimental OPLC separation unit 100 (OSU 100) has been used for fully on-line multiple hyphenation using the...     

GlycoMiner: a new software tool to elucidate glycopeptide composition

New computer software, GlycoMiner, has been developed to automatically identify tandem (MS/MS) spectra obtained in liquid chromatography/mass spectrometry (LC/MS) runs which correspond to N-glycopeptides. The program complements conventional proteomics analysis, and can be used in a high-throughput environment. The program interprets the spectra and determines the structure of the corresponding glycopeptides. GlycoMiner runs under Windows, can process spectra obtained on various instruments, and can be downloaded from our website (w3.chemres.hu/ms/glycominer). The algorithm works similarly to a human expert; evaluates the low mass oxonium ions; deduces oligosaccharide losses from the protonated molecule; and identifies the mass of the peptide residue. The program has been tested on tryptic digests of two glycopeptides: AGP (which has five different N-glycosylation sites) and transferrin (with two N-glycosylation sites). Results have been evaluated both manually and by GlycoMiner. Out of 3132 MS/MS spectra 338 were found to correspond to glycopeptides; identification by GlycoMiner showed a 0.1% false positive and 0.1% false negative rate. From these it was possible to identify 196 glycan structures manually; GlycoMiner correctly identified all of these, with no false positives. The rest were low quality spectra, not suitable for structure assignment.     

LC-DAD and LC–MS–MS Analysis of Piperidine Alkaloids of Lobelia inflata L. (In Vitro and In Vivo)

An LC-DAD method was developed for determination of lobeline from in vitro and in vivo cultures of Lobelia inflata. Samples were extracted with 0.1 N HCl–acetonitrile (1:1, v/v), and purified by solid-phase extraction. Optimized conditions resulted in high recovery. LC separations were performed on an Eurosphere C8 reversed-phase column using 30:70 (v/v) acetonitrile–0.1% trifluoroacetic acid as a mobile phase. Quantitative determination of lobeline was performed by external standard method at 250 nm, in the range of 2.4–80 μg mL⁻¹. Validation studies proved that the repeatability of the method was good and the recovery was satisfactory. In vitro organized cultures contained considerable amount of lobeline (herb: 175 μg g⁻¹, root: 100 μg g⁻¹). When these cultures were transplanted into the open field, the lobeline content increased significantly (herb: 323 μg g⁻¹, root: 833 μg g⁻¹). Plants obtained from seed propagation contained 382 μg g⁻¹ lobeline in the herb. For direct characterization of di-substituted piperidine alkaloids in extracts of L. inflata, tandem mass spectrometric method was developed using electrospray ionization. Analysis was performed in the positive ion mode on a triple quadropole LC–MS system. LC separations were achieved on Eurosphere C8 column with a modified mobile phase (acetonitrile–30 mM ammonium formate, pH 2.80) to ensure proper molecular ionization. The identification and structural elucidation of the alkaloids were performed by comparing their changes in molecular mass (ΔM), full-scan MS–MS spectra with those of lobeline, norlobelanine and lobelanidine. These alkaloids and ten other derivatives were identified in the plant extracts. Three piperidine alkaloids were reported in L. inflata for the first time.

     

Fragmentation‐related phosphinylations using 2‐aryl‐2‐phosphabicyclo[2.2.2]oct‐ 5‐ene‐ and ‐octa‐5,7‐diene 2‐oxides

A series of new P‐methylphenyl P‐heterocycles are introduced. The para and ortho substituted 2,5‐dihydro‐1H‐phosphole oxides ( 1a and 1b ) were converted to the double‐bond isomers ( A and B ) of 1,2‐dihydrophosphinine oxides ( 3a and 3b ) via the corresponding phosphabicyclo[3.1.0]hexane oxides ( 2a or 2b ). Isomeric mixture ( A and B ) of the dihydrophosphinine oxides ( 3a and 3b ) gave, in turn, the isomers ( A and B ) of phosphabicyclo[2.2.2]oct‐5‐enes ( 4a and 4b ) or a phosphabicyclo[2.2.2]octa‐5,7‐diene ( 5 ) in Diels‐Alder reaction with dienophiles. The bridged P‐heterocycles ( 4 and 5 ) were useful in the photo‐ or thermoinduced fragmentation‐related phosphinylation of hydroxy compounds and amines. The new precursors ( 4a and 4b ) were applied in mechanistic investigations. © 2003 Wiley Periodicals, Inc. Heteroatom Chem 14:443–451, 2003; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/hc.10176     

Competitive [4 + 2] cycloadditions in equimolar mixtures of 1‐arylphosphole oxides

Four different [4 + 2] cycloadditions were observed to take place in the equimolar mixtures of two different arylphosphole oxides 2a + 2b or 2b + 2c . In addition to the phosphole oxide dimers 3a‐a and 3b‐b , or 3b‐b and 3c‐c , the crossed cycloadducts 3a‐b and 3b‐a , or 3b‐c and 3c‐b were also formed in considerable portions. © 2001 John Wiley & Sons, Inc. Heteroatom Chem 12:633–635, 2001     

Qualitative behaviour of a ratio-dependent predator–prey system

This paper deals with the qualitative properties of an autonomous system of differential equations, modeling ratio-dependent predator–prey interactions.This model differs from traditional ratio dependent models essentially in the predator mortality term, the death rate of the predator is not constant but instead increases when there is overcrowding.We incorporate delay(s) into the system. The most important observation is that as the delay(s) is (are) increased the originally asymptotic stable interior equilibrium loses its stability. Furthermore at a certain critical value a Hopf bifurcation takes place: small amplitude periodic solutions arise.     

Accurate measurement of long-range heteronuclear coupling constants from undistorted multiplets of an enhanced CPMG-HSQMBC experiment

Here, we present a modified CPMG-HSQMBC experiment which is capable to reduce the detrimental phase twists in the "long-range" connectivity multiplets caused by proton-proton couplings. We demonstrate that concerted CPMG pulse trains applied on both nuclei in the starting CPMG-INEPT transfer step can considerably be improved by composite pi pulses that compensate for pulse imperfections and off-resonance effects. Experimental optimization of the interpulse delay within the CPMG cycle was found to be crucial in order to achieve the best possible "decoupling" of homonuclear coupling modulation.     

Quantitative Comparison of Tandem Mass Spectra Obtained on Various Instruments

The similarity between two tandem mass spectra, which were measured on different instruments, was compared quantitatively using the similarity index (SI), defined as the dot product of the square root of peak intensities in the respective spectra. This function was found to be useful for comparing energy-dependent tandem mass spectra obtained on various instruments. Spectral comparisons show the similarity index in a 2D “heat map”, indicating which collision energy combinations result in similar spectra, and how good this agreement is. The results and methodology can be used in the pharma industry to design experiments and equipment well suited for good reproducibility. We suggest that to get good long-term reproducibility, it is best to adjust the collision energy to yield a spectrum very similar to a reference spectrum. It is likely to yield better results than using the same tuning file, which, for example, does not take into account that contamination of the ion source due to extended use may influence instrument tuning. The methodology may be used to characterize energy dependence on various instrument types, to optimize instrumentation, and to study the influence or correlation between various experimental parameters.

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