DYNGA: a general purpose QM-MM-MD program. I. Application to water

We present a general purpose QM-MM-MD engine (DYNGA) designed to test alternative hybrid Hamiltonians geared towards the treatment of problems of interest in structural biology including the use of experimental data constraints. In this first presentation we use DYNGA to explore the behaviour of a traditional QM-MM approach in the treatment of the water—water interaction. We find the potential energy hypersurface for the water dimer computed with the HF 4–31G*/TIP3P hybrid Hamiltonian tends to be too flat. We also explore the effect of using traditional QM-MM techniques on proton wires and conclude there is a need for improvement, possibly addressed by using polarizable force fields.     

Identification of nerve agents and their homologues and dialkyl methylphosphonates by gas chromatography/fourier transform infrared spectrometry (GC-FTIR)

GC-Direct deposition-FTIR spectra of 55 nerve agent homologues and dialkyl methylphosphonates were analysed. Spectral features of these compounds are discussed. A method is proposed for identification of the alkyl and alkoxy groups of compounds belonging to sarin, tabun or dialkyl methylphosphonates families.     

ConFlo III - an interface for high precision delta(13)C and delta(15)N analysis with an extended dynamic range

A newly developed interface coupling a CHN combustion device (elemental analyser 'EA') to an isotope ratio mass spectrometer is described and evaluated. The purpose of the device is to extend the dynamic range of delta(13)C and delta(15)N analysis from less than 2 orders of magnitude to more than 3 orders of magnitude. Carbon isotope ratio measurements of atropine as a model compound have been performed analysing between 1 μg to 5 mg C with acceptable to excellent precision (0.6 to 0.06 per thousand, delta-notation). The correction due to the blank signal is critical for sample amounts smaller than 4 μg C. The maximum sample weight is determined by the combustion capacity of the EA. Larger sample amounts are measured using dilution of a small part of the EA effluent with helium. The dilution mechanism works virtually free of isotope fractionation. Copyright 1999 John Wiley & Sons, Ltd.     

Optimization of capillary electrophoretic-electrospray ionization-mass spectrometric analysis of catecholamines

The capillary electrophoretic-mass spectrometric analysis (CE-MS) of catecholamines was optimized with coaxial sheath flow interface and electrospray ionization (ESI). The parameters studied included the sheath liquid composition and its flow rate, separation conditions in ammonium acetate buffer together with the ESI and cone voltages as mass spectrometric parameters. In addition, the effect of ESI voltage on injection as well as the siphoning effect were considered. The optimized conditions were a sheath liquid composition of methanol-water (80:20 v/v) with 0.5% acetic acid, with a flow rate of 6 microL/min. The capillary electrophoretic separation parameters were optimized with 50 mM ammonium acetate buffer, pH 4.0, to +25 kV separation voltage together with a pressure of 0.1 psi. The most intensive signals were obtained with an ESI voltage of +4.0 kV and a cone voltage of +20 V. The nonactive ESI voltage during injection as well as avoidance of the siphoning effect increased the sensitivity of the MS detection considerably. The use of ammonium hydroxide as the CE capillary conditioning solution instead of sodium hydroxide did not affect the CE-MS performance, but allowed the conditioning of the capillary between analyses to be performed in the MS without contaminating the ion source.     

Feasibility of using atmospheric pressure matrix-assisted laser desorption/ionization with ion trap mass spectrometry in the analysis of acetylated xylooligosaccharides derived from hardwoods and Arabidopsis thaliana

The atmospheric pressure matrix-assisted laser desorption/ionization with ion trap mass spectrometry (AP-MALDI-ITMS) was investigated for its ability to analyse plant-derived oligosaccharides. The AP-MALDI-ITMS was able to detect xylooligosaccharides (XOS) with chain length of up to ten xylopyranosyl residues. Though the conventional MALDI–time-of-flight/mass spectrometry (TOF/MS) showed better sensitivity at higher mass range (>m/z 2,000), the AP-MALDI-ITMS seems to be more suitable for detection of acetylated XOS, and the measurement also corresponded better than the MALDI-TOF/MS analysis to the actual compositions of the pentose- and hexose-derived oligosaccharides in a complex sample. The structures of two isomeric aldotetrauronic acids and a mixture of acidic XOS were elucidated by AP-MALDI-ITMS using multi-stages mass fragmentation up to MS³. Thus, the AP-MALDI-ITMS demonstrated an advantage in determining both mass and structures of plant-derived oligosaccharides. In addition, the method of combining the direct endo-1,4-β-d-xylanase hydrolysis of plant material, and then followed by AP-MALDI-ITMS detection, was shown to recognize the substitution variations of glucuronoxylans in hardwood species and in Arabidopsis thaliana. To our knowledge, this is the first report to demonstrate the acetylation of glucuronoxylan in A. thaliana. The method, which requires only a small amount of plant material, such as 1 to 5 mg for the A. thaliana stem material, can be applied as a high throughput fingerprinting tool for the fast comparison of glucuronoxylan structures among plant species or transformants that result from in vivo cell wall modification.     

Comparison of different methods for the determination of volatile organic compounds in water samples

The aim of this work was to compare the characteristics of three methods, membrane inlet mass spectrometry (MIMS), purge-and-trap gas chromatography-mass spectrometry (P&T) and static headspace gas chromatography (HSGC), for the determination of volatile organic compounds in water samples as used in routine analysis. The characteristics examined included linear dynamic ranges, detection limits of selected environmentally hazardous volatile organic compounds (e.g. toluene, benzene and trichloroethene) in water, required analysis time and reproducibility of the analytical methods. The MIMS and P&T methods had the lowest detection limits for all the tested compounds, ranging from 0.1 to 5 mug 1(-1). Linear dynamic ranges using the MIMS method were about four orders of magnitude and using the P&T method about two orders of magnitude. Detection limits of the HSGC method were 10-100 times higher than those of the other two methods, but the linear dynamic ranges were larger, even up to six orders of magnitude. The analysis time per sample was shortest for the MIMS method, from 5 to 10 min, and ranged around from 35 to 45 min for the HSGC and P&T methods. The reproducibilities of the methods were of the same order of magnitude, in the range of 1-13%. Agreement between the analytical results obtained for spiked samples and for environmental water samples by the three different methods was very good.     

Utilization of a multimembrane inlet and a cyclic sudden sampling introduction mode in membrane inlet mass spectrometry

Sudden sampling introduction into a membrane inlet mass spectrometer (MIMS) considerably improves the selectivity of the membrane inlet and is therefore applicable even for compounds with low permeabilities through a silicone membrane. In this study the basics of cyclic non-steady-state sudden increase sample injection were studied using a three-membrane inlet and a portable sector double-focusing mass spectrometer. The operational parameters of the inlet system providing the most efficient enrichment of volatile organic compounds (VOCs) in air were defined. Simulation of the diffusion process following sudden sample introduction into the three-membrane inlet was also carried out. Experimental testing of the three-membrane inlet system with the cyclic sudden sample injection mode for benzene, toluene, styrene, and xylene in air was performed. The simulation and the experimental results demonstrated that, when this mode is used, the VOCs/nitrogen relative enrichment factor of samples introduced into the mass spectrometer equipped with a three-membrane inlet is increased by a factor of approximately 10(5) compared with a direct introduction method. This effect may be used to decrease detection limits of compounds obtained with mass spectrometry to decrease matrix flow through the inlet at the same detection limits.