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Vilnius, Lithuania

Antler M.,ACD Labs Inc.
Reading for the R and D Community

Mass spectrometry (MS) instrument vendors offer automated MS/MS data collection for analytes that are present above a certain intensity threshold, or for expected metabolites. ACD/Labs have developed ACD/Metabolite ID Suite™ that generates a report of retention times, peak areas, and spectra for each expected metabolite. Additional software modules can predict metabolite structures for a new drug, identifying the sites most likely to be susceptible to metabolism by human liver microsomes, which can help with both structure elucidation and drug design. The ACD/Metabolite ID Suite™ can help extract the likely metabolite peaks from a complex full-scan liquid chromatography-mass chromatography (LC/MS) data set. The software can compare the metabolized sample with a control sample and identify unique features in the metabolized sample. Software reduces the complex data set to a short list of peaks for further review, interprets the spectrum to determine the mass of the protonated molecule, and determines potential chemical formulae for the potential metabolite. Source

Samokhin A.,Moscow State University | Sotnezova K.,Moscow State University | Lashin V.,ACD Labs Inc. | Revelsky I.,Moscow State University
Journal of Mass Spectrometry

Performance of several library search algorithms (against EI mass spectral databases) implemented in commercial software products (acd/specdb, chemstation, gc/ms solution and ms search) was estimated. Test set contained 1000 mass spectra, which were randomly selected from NIST'08 (RepLib) mass spectral database. It was shown that composite (also known as identity) algorithm implemented in ms search (NIST) software gives statistically the best results: the correct compound occupied the first position in the list of possible candidates in 81% of cases; the correct compound was within the list of top ten candidates in 98% of cases. It was found that use of presearch option can lead to rejection of the correct answer from the list of possible candidates (therefore presearch option should not be used, if possible). Overall performance of library search algorithms was estimated using receiver operating characteristic curves. © 2015 John Wiley & Sons, Ltd. Source

Ovenden S.P.B.,Defence Science and Technology Organisation, Australia | Nielson J.L.,ACD Labs Inc. | Liptrot C.H.,James Cook University | Willis R.H.,Australian Institute of Marine Science | And 3 more authors.

The methanol extract of an assemblage of Halimeda stuposa and a Dictyota sp., yielded three natural products characteristic of Dictyota sp., and one of Halimeda sp. These included the xenicane diterpene 4-hydroxydictyolactone (1), and the diterpenes dictyol E (2), 8a,11-dihydroxypachydictyol A (3) and indole-3-carboxaldehyde (4). A minor revision of 1 and new spectroscopic data for 1 and 2 are provided, along with associated anti-cancer activities of compounds 1-4. © 2012 by the authors. Source

Aidas K.,VsI Aukstieji algoritmai A. Mickeviciaus g. 29LT 08117Vilnius Lithuania | Lanevskij K.,VsI Aukstieji algoritmai A. Mickeviciaus g. 29LT 08117Vilnius Lithuania | Kubilius R.,VsI Aukstieji algoritmai A. Mickeviciaus g. 29LT 08117Vilnius Lithuania | Juska L.,VsI Aukstieji algoritmai A. Mickeviciaus g. 29LT 08117Vilnius Lithuania | Japertas P.,ACD Labs Inc.
Journal of Computational Chemistry

Aqueous pKa of selected primary benzenesulfonamides are predicted in a systematic manner using density functional theory methods and the SMD solvent model together with direct and proton exchange thermodynamic cycles. Some test calculations were also performed using high-level composite CBS-QB3 approach. The direct scheme generally does not yield a satisfactory agreement between calculated and measured acidities due to a severe overestimation of the Gibbs free energy changes of the gas-phase deprotonation reaction by the used exchange-correlation functionals. The relative pKa values calculated using proton exchange method compare to experimental data very well in both qualitative and quantitative terms, with a mean absolute error of about 0.4 pKa units. To achieve this accuracy, we find it mandatory to perform geometry optimization of the neutral and anionic species in the gas and solution phases separately, because different conformations are stabilized in these two cases. We have attempted to evaluate the effect of the conformer-averaged free energies in the pKa predictions, and the general conclusion is that this procedure is highly too costly as compared with the very small improvement we have gained. © 2015 Wiley Periodicals, Inc. Source

Euerby M.R.,HiChrom Ltd. | Euerby M.R.,University of Strathclyde | Hulse J.,HiChrom Ltd. | Petersson P.,Novo Nordisk AS | And 2 more authors.
Analytical and Bioanalytical Chemistry

The retention behaviour of acidic, basic and quaternary ammonium salts and polar neutral analytes has been evaluated on acidic, basic and neutral hydrophilic interaction chromatography (HILIC) stationary phases as a function of HILIC operating parameters such as MeCN content, buffer concentration, pH and temperature. Numerous empirical HILIC retention models (existing and newly developed ones) have been assessed for their ability to describe retention as a function of the HILIC operating parameters investigated. Retention models have been incorporated into a commercially available retention modelling programme (i.e. ACD/LC simulator) and their accuracy of retention prediction assessed. The applicability of HILIC modelling using these equations has been demonstrated in the two-dimensional isocratic (i.e. buffer concentration versus MeCN content modelling) and one-dimensional gradient separations for a range of analytes of differing physico-chemical properties on the three stationary phases. The accuracy of retention and peak width prediction was observed to be comparable to that reported in reversed-phase chromatography (RPC) retention modelling. Intriguingly, our results have confirmed that the use of gradient modelling to predict HILIC isocratic conditions and vice versa is not reliable. A relative ranking of the importance of the retention and selectivity of HILIC operating parameters has been determined using statistical approaches. For retention, the order of importance was observed to be organic content > stationary phase > temperature ≈ mobile phase pH (i.e. pH 3-6 which mainly effects the ionization of the analyte) ≈ buffer concentration. For selectivity, the nature of the stationary phase > mobile phase pH > buffer concentration > temperature > organic content. © 2015 Springer-Verlag Berlin Heidelberg. Source

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