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Selected AbstractsSubstituent effects in the Baeyer,Villiger reaction of acetophenones: a theoretical studyJOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 7 2009Lino Reyes Abstract This paper reports the first complete theoretical study of substituent effects on the mechanism of the Baeyer, Villiger (BV) reaction in non-polar solvents taking into account the lowest-energy mechanism that has been proposed for this rearrangement which is non-ionic and fully concerted. The BV reaction of p -substituted acetophenones, p -XC6H4COCH3 (X,=,NO2, CN, H, CH3, OCH3), with performic (PFA) and trifluoroperacetic (TFPAA) acids, catalyzed by formic (FA) and trifluoroacetic (TFAA) acids, respectively, using the MPWB1K functional and the 6-311G(d,p) and 6-311++G(d,p) basis sets, are studied. Solvent effects are taken into account by means of the PCM continuum model using dichloromethane as solvent. Electron-donating substituents on the aryl group have a relatively small activation effect on the first step, but a pronounced activation effect on the second to the point of being able to change the rate-determining step (RDS) of the reaction, as observed in the case of p -methoxyacetophenone with TFPAA acids. After analyzing the changes in Gibbs free energy of activation, geometrical parameters, and charge distributions of the transition states (TSs), explanations are provided for the two distinct effects that substituents on the ketone have on the kinetics of the addition and migration steps of the BV oxidation. The effect of the acid/peracid pair used is also discussed. Copyright © 2008 John Wiley & Sons, Ltd. [source] T1 corrected B1 mapping using multi-TR gradient echo sequencesMAGNETIC RESONANCE IN MEDICINE, Issue 3 2010Tobias Voigt Abstract This work presents a new approach toward a fast, simultaneous amplitude of radiofrequency field (B1) and T1 mapping technique. The new method is based on the "actual flip angle imaging" (AFI) sequence. However, the single pulse repetition time (TR) pair used in the standard AFI sequence is replaced by multiple pulse repetition time sets. The resulting method was called "multiple TR B1/T1 mapping" (MTM). In this study, MTM was investigated and compared to standard AFI in simulations and experiments. Feasibility and reliability of MTM were proven in phantom and in vivo experiments. Error propagation theory was applied to identify optimal sequence parameters and to facilitate a systematic noise comparison to standard AFI. In terms of accuracy and signal-to-noise ratio, the presented method outperforms standard AFI B1 mapping over a wide range of T1. Finally, the capability of MTM to determine T1 was analyzed qualitatively and quantitatively, yielding good agreement with reference measurements. Magn Reson Med, 2010. © 2010 Wiley-Liss, Inc. [source] PCR primers for identification of Sirococcus conigenus and S. tsugae, and detection of S. conigenus from symptomatic and asymptomatic red pine shootsFOREST PATHOLOGY, Issue 3 2008D. R. Smith Summary Regions of diversity in the internal transcribed spacer (ITS) sequences of Sirococcus species were exploited to design primer pairs used in a PCR-based method for the identification of the conifer shoot blight pathogen Sirococcus conigenus and the closely related fungus Sirococcus tsugae. The specificity of each primer pair for the respective fungus, detection limits and utility for detection from host material were confirmed. The S. conigenus primers were then used to detect this pathogen in tissues of symptomatic or apparently healthy red pine shoots collected at six locations in Wisconsin and Michigan and results compared with those obtained using a cultural assay. For needles, bark and wood of symptomatic shoots, the mean frequencies of detection of S. conigenus using the PCR-based methods were consistent (,7.5 out of 10) and always greater than for the cultural assay. Detection from symptomatic shoots using the cultural assay was more frequent from needles than from bark or wood. Both the PCR-based method and the cultural assay detected S. conigenus in similar frequencies from asymptomatic shoots, although less frequently than from symptomatic shoots. The efficiency of the PCR-based method and its utility for direct testing of host material should make it particularly useful in areas where multiple shoot blight pathogens are found. [source] Prediction of integral membrane protein type by collocated hydrophobic amino acid pairsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 1 2009Ke Chen Abstract A computational model, IMP-TYPE, is proposed for the classification of five types of integral membrane proteins from protein sequence. The proposed model aims not only at providing accurate predictions but most importantly it incorporates interesting and transparent biological patterns. When contrasted with the best-performing existing models, IMP-TYPE reduces the error rates of these methods by 19 and 34% for two out-of-sample tests performed on benchmark datasets. Our empirical evaluations also show that the proposed method provides even bigger improvements, i.e., 29 and 45% error rate reductions, when predictions are performed for sequences that share low (40%) identity with sequences from the training dataset. We also show that IMP-TYPE can be used in a standalone mode, i.e., it duplicates significant majority of correct predictions provided by other leading methods, while providing additional correct predictions which are incorrectly classified by the other methods. Our method computes predictions using a Support Vector Machine classifier that takes feature-based encoded sequence as its input. The input feature set includes hydrophobic AA pairs, which were selected by utilizing a consensus of three feature selection algorithms. The hydrophobic residues that build up the AA pairs used by our method are shown to be associated with the formation of transmembrane helices in a few recent studies concerning integral membrane proteins. Our study also indicates that Met and Phe display a certain degree of hydrophobicity, which may be more crucial than their polarity or aromaticity when they occur in the transmembrane segments. This conclusion is supported by a recent study on potential of mean force for membrane protein folding and a study of scales for membrane propensity of amino acids. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009 [source] | ||||||||||