Ion trap tandem mass spectrometry applied to small multiply charged oligonucleotides with a modified base

Two isomeric oligodeoxynucleotide hexamers, 5′-d(N-6meATGCAT)-3′ and 5′-d(ATGSmeCAT)-3′, were subjected to analysis by electrospray and ion trap mass spectrometry. In the case of the isomer with a modified adenine, location of the modified base in the sequence was straightforward and a triple mass spectrometry experiment provided information on the identity of the modification. In contrast, the isomer with the methylated cytosine did not yield definitive information on the location or identity of the modification. Tandem mass spectrometry data in this case could indicate that the modification was present on either the third or fourth nucleoside. The two isomers represent extremes in the facility with which modified bases can be identified and located in a small oligonucleotide via multiple mass spectrometry of multiply charged anions. A preference for loss of particular bases strongly influences which structurally diagnostic ions are formed upon collisional activation. The likelihood for locating and identifying a modified base is dependent, therefore, upon the likelihood that the base is lost directly from the parention.     

Accurate grading of brain gliomas by soft independent modeling of class analogy based on non‐negative matrix factorization of proton magnetic resonance spectra

Hydrogen magnetic resonance spectroscopy (¹H‐MRS) is a non‐invasive technique which provides a ‘frequency‐signal intensity’ spectrum of biochemical compounds of tissues in the body. Although this method is currently used in human brain studies, accurate classification of in‐vivo ¹H‐MRS is a challenging task in the diagnosis of brain tumors. Problems such as overlapping metabolite peaks, incomplete information on background component and low signal‐to‐noise ratio disturb classification results of this spectroscopic method. This study presents an alternative approach to the soft independent modeling of class analogy (SIMCA) technique, using non‐negative matrix factorization (NMF) for dimensionality reduction. In the adopted strategy, the performance of SIMCA was improved by application of a robust algorithm for classification in the presence of noisy measurements. Total of 219 spectra from two databases were taken by water‐suppressed short echo‐time ¹H‐MRS, acquired from different subjects with different stages of glial brain tumors (Grade II (26 cases), grade III (24 cases), grade IV (41 cases), as well as 25 healthy cases). The SIMCA was performed using two approaches: (i) principal component analysis (PCA) and (ii) non‐negative matrix factorization (NMF), as a modified approach. Square prediction error was considered to assess the class membership of the external validation set. Finally, several figures of merit such as the correct classification rate (CCR), sensitivity and specificity were calculated. Results of SIMCA based on NMF showed significant improvement in percentage of correctly classified samples, 91.4% versus 83.5% for PCA‐based model in an independent test set. Copyright © 2015 John Wiley & Sons, Ltd.     

Synthesis and biological activity of Magnesium(II) complexes of heptaaza Schiff base macrocyclic ligands; 1H and 13C chemical shifts computed by the GIAO-DFT and CSGT-DFT methodologies

Two new pendant armed Schiff base macrocyclic complexes, [MgL¹](ClO₄)₂ (1), and [MgL²](ClO₄)₂ (2), have been prepared via cyclocondensation of 2,6-diformylpyridine and 2,6-diacetylpyridine with two hexadentate hexaamines, ten and tmen, in the presence of Mg(II) ion. The ligands are 15-membered pentaaza macrocycles having two 2-aminoethyl pendant arms. The newly prepared complexes are investigated by IR, ¹H NMR, ¹³C{¹H} NMR, DEPT(135), COSY(H, H) and HMQC spectroscopic methods. The antimicrobial screening of newly prepared complexes, 1 and 2, as well as previously prepared similar complexes, [MgL³](ClO₄)₂ (3) and [MgL⁴](ClO₄)₂ (4), against Escherichia coli, Staphylococcus aureus and candidia albicans showed that the macrocyclic complexes of Mg(II) containing 15-membered pentaaza ring (1, 2 and 3) have no activity. Where as the compound 4, which contain 16-membered pentaaza ring, had remarkable inhibition zone on the culture of S. aureus and E. coli as compared with standard drugs. The ¹H and ¹³C chemical shieldings of gas phase complexes were also studied by the gauge independent atomic orbital (GIAO) and continuous set of gauge transformations (CSGT) methods at the level of density functional theory (DFT). The computed ¹³C chemical shifts are in reasonably good agreement with the experimental data.     

Synthesis, characterization, biological and thermal studies of Cu(II) complexes of salen and tetrahedrosalen ligands

A series of mononuclear salen type copper(II) complexes, [CuLⁿ] (n = 1–4), and their corresponding tetrahydrosalen complexes, [CuH₂Lⁿ] (n = 1,2) were prepared by the reaction of the N₂O₂ ligands with Cu(II) ion in ethanol, where H₂L¹ = N,N-bis(3,5-di-tert-butylsalicylidene)-2,2-dimethyle-1,3-diaminopropan, H₂L² = N,N-bis(3,5-di-tert-butylsalicylidene)-1,2-diaminopropane, H₂L³ = N,N-bis(4-methoxysalicylidene)-2,2-dimethyle-1,3-diaminopropan; H₂L⁴ = N,N-bis(4-methoxysalicylidene)-1,2-diaminopropane, H₂[H₂L¹] = N,N-bis(2-hydroxyl-3,5-di-tert-butylphenyl)-2,2-dimethyle-1,3-diaminopropan and H₂[H₂L²] = N,N-bis(2-hydroxyl-3,5-di-tert-butylphenyl)-1,2-diaminopropane. The prepared ligands and complexes were characterized by the combination of IR, UV-Vis, NMR (as far as possible), elemental and thermal analyses. All prepared compounds were also evaluated for their antibacterial (Escherichia coli and Staphylococcus aureus) and antifungal (Candida albicans) activities by the disc diffusion method. The compounds were found have no remarkable antimicrobial activities.     

Liquid Phase Selective Oxidation of Alcohols over VPO Catalysts Supported on Mesoporous Hexagonal Molecular Sieves (HMS)

The vanadium phosphorous oxide (VPO) catalysts, supported on mesoporous hexagonal molecular sieves (HMS) with different vanadium loadings, were prepared by precipitation method on organic phase. Techniques such as XRD, BET and SEM, were used for characterization of the catalyst. The bulk VPO catalyst contains vanadyl pyrophosphate phase ((VO)₂P₂O₇), and a small amount of VOPO₄. The high surface area, large pore volume and pore size of HMS in VPO/HMS samples, provide an excellent dispersion of same phase of VPO compound on the support surface. Oxidation of various alcohols was studied in the liquid phase over VPO/HMS catalyst, using tert‐butylhydroperoxide (TBHP) as an oxidant. The activity of VPO/HMS samples were considerably increased with respect to bulk VPO catalyst. At 90 °C, the obtained activities were 0.567 and 6.545 g_pro.g^?1_VPOh^?1 over the bulk VPO and 20 wt% VPO/HMS catalysts, respectively. The effects of substrates, reaction time, reaction temperature, solvents, catalyst recycling and leaching of VPO in liquid phase reaction were also investigated. The following order has been observed for the percentage of conversions of alcohols: Benzylic alcohol > Secondary alcohol ～ Primary alcohol. The kinetic of benzyl alcohol oxidation using excess TBHP over VPO/HMS catalyst was investigated at temperatures of 27, 60 and 90 °C, and followed a pseudo‐first order with respect to benzyl alcohol.     

Generating strong defining hyperplanes of the production possibility set in data envelopment analysis

In data envelopment analysis (DEA), identification of the strong defining hyperplanes of the empirical production possibility set (PPS) is important, because they can be used for determining rates of change of outputs with change in inputs. Also, efficient hyperplanes determine the nature of returns to scale. The present work proposes a method for generating all linearly independent strong defining hyperplanes (LISDHs) of the PPS passing through a specific decision making unit (DMU). To this end, corresponding to each efficient unit, a perturbed inefficient unit will be defined and, using at most m+s linear programs, all LISDHs passing through the DMU will be determined, where m and s are the numbers of inputs and outputs, respectively.     

Chromatographic resolution and isotherm determination of (R,S)-mandelic acid on Chiralcel-OD column

Resolution of racemic mandelic acid ((R,S)-MA) and numerical determination of binary competitive isotherm of (R,S)-MA on Chiralcel-OD column have been investigated in this study. The effects of the alcohol modifier and acidic additive in the mobile phase on the retention and enantioseparation of (R,S)-MA were studied at first. The inverse method was then used to determine the competitive isotherm parameters of (R,S)-MA by minimizing the sum of square deviations of the model predictions from the measured elution profiles. The results indicate that the mobile phase with 85% hexane/15% isopropanol/0.3% trifluoroacetic acid mixture gives the best resolution of (R,S)-MA and competitive-modified Langmuir isotherm provides the more accurate sorption mechanism of (R,S)-MA on the cellulose tris(3,5-dimethylphenylcarbamate) chiral stationary phase.