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Structural Identification (structural + identification)
Selected AbstractsStructural Identification of Spectroscopic Substates in NeuroglobinCHEMPHYSCHEM, Issue 1 2010Karin Nienhaus Dr. Abstract The structural origins of infrared absorptions of photodissociated CO in murine neuroglobin (Ngb) are determined by combining Fourier transform infrared (FTIR) spectroscopy and molecular dynamics (MD) simulations. Such an approach allows to identify and characterize both the different conformations of the Ngb active site and the transient ligand docking sites. To capture the influence of the protein environment on the spectroscopy and dynamics, experiments and simulations are carried out for the wild type protein and its F28L and F28W mutants. It is found that a voluminous side chain at position 28 divides site B into two subsites, B' and B". At low temperatures, CO in wt Ngb only migrates to site B' from where it can rebind, and B" is not populated. The spectra of CO in site B' for wt Ngb from simulations and experiments are very similar in spectral shift and shape. They both show doublets, red-shifted with respect to gas-phase CO and split by,8 cm,1. The FTIR spectra of the F28L mutant show additional bands which are also found in the simulations and can be attributed to CO located in substate B". The different bands are mainly related to different orientations of the His64 side chain with respect to the CO ligand. Large red-shifts arise from strong interactions between the HistidineNH and the CO oxygen. After dissociation from the heme iron, the CO ligand visits multiple docking sites. The locations of the primary docking site B and a secondary site C, which corresponds to the Mb Xe4 cavity, could be identified unambiguously. Finally, by comparing experiment and simulations it is also possible to identify protonation of its , position (His,64 NgbCO) as the preferred heme-bound conformation in the wild type protein with a signal at 1935 cm,1. [source] Structural identification of trace level enol tautomer impurity by on-line hydrogen/deuterium exchange HR-LC/MS in a LTQ-Orbitrap hybrid mass spectrometerJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 7 2007Dr Guodong Chen Guodong Chen [source] Structural characterization and identification of ecdysteroids from Sida rhombifolia L. in positive electrospray ionization by tandem mass spectrometryRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 16 2008Yan-Hong Wang Seven ecdysteroids isolated from Sida rhombifolia L. were studied by electrospray ionization multi-stage tandem mass spectrometry (ESI-MSn) in the positive ion mode using an ion trap analyzer and high-performance liquid chromatography coupled with a diode-array detector (HPLC/DAD). The HPLC experiments were performed by means of a reversed-phase C18 column and a binary mobile phase system consisting of water (containing 0.05% formic acid) and acetonitrile (containing 0.05% formic acid) under gradient elution conditions. According to mass spectral features and the substitution at C-2, C-20, C-24 and C-25, ecdysteroids in S. rhombifolia were classified into three sub-groups. Structural identification of these three sub-groups of ecdysteroids was established by LC/multi-stage ion trap mass spectrometry on-line or off-line. The fragmentation patterns of ecdysteroids yielded ions of successive loss of 1,4 water molecules. Furthermore, ions corresponding to the complete loss of the side chain at C-17 will help to identify the sub-groups of ecdysteroids in addition to containing a hydroxyl moiety at one of the above-mentioned positions. Based on the HPLC retention behavior, the diagnostic UV spectra and the molecular structural information provided by ESI-MSn spectra, a total of nine naturally occurring ecdysteroids were identified, of these two are identified for the first time in S. rhombifolia. Copyright © 2008 John Wiley & Sons, Ltd. [source] Output-only structural identification in time domain: Numerical and experimental studiesEARTHQUAKE ENGINEERING AND STRUCTURAL DYNAMICS, Issue 4 2008M. J. Perry Abstract By identifying changes in stiffness parameters, structural damage can be detected and monitored. Although considerable progress has been made in this research area, many challenges remain in achieving robust structural identification based on incomplete and noisy measurement signals. The identification task is made even more difficult if measurement of input force is to be eliminated. To this end, an output-only structural identification strategy is proposed to identify unknown stiffness and damping parameters. A non-classical approach based on genetic algorithms (GAs) is adopted. The proposed strategy makes use of the recently developed GA-based method of search space reduction, which has shown to be able to accurately and reliably identify structural parameters from measured input and output signals. By modifying the numerical integration scheme, input can be computed as the parameter identification task is in progress, thereby eliminating the need to measure forces. Numerical and experimental results demonstrate the power of the strategy in accurate and efficient identification of structural parameters and damage using only incomplete acceleration measurements. Copyright © 2007 John Wiley & Sons, Ltd. [source] A neural network approach for structural identification and diagnosis of a building from seismic response dataEARTHQUAKE ENGINEERING AND STRUCTURAL DYNAMICS, Issue 2 2003C. S. Huang Abstract This work presents a novel procedure for identifying the dynamic characteristics of a building and diagnosing whether the building has been damaged by earthquakes, using a back-propagation neural network approach. The dynamic characteristics are directly evaluated from the weighting matrices of the neural network trained by observed acceleration responses and input base excitations. Whether the building is damaged under a large earthquake is assessed by comparing the modal parameters and responses for this large earthquake with those for a small earthquake that has not caused this building any damage. The feasibility of the approach is demonstrated through processing the dynamic responses of a five-storey steel frame, subjected to different strengths of the Kobe earthquake, in shaking table tests. Copyright © 2002 John Wiley & Sons, Ltd. [source] The bioactivity-guided isolation and structural identification of toxic cucurbitacin steroidal glucosides from stemodia kingiiPHYTOCHEMICAL ANALYSIS, Issue 4 2006Jeremy G. Allen Abstract A histologically validated murine model for the ovine intoxication by Stemodia kingii was used as a bioassay to guide the isolation of several groups of toxins from Stemodia kingii. Two of the toxins from one group were purified sufficiently to allow structural analysis and a determination of their median lethal doses (LD50) for oral administration to mice. A combination of acid hydrolysis, elemental analysis, HPLC-MS, 1D-NMR (1H, 13C) and 2D-NMR (1H,1H COSY, 13C,1H HSQC and HMBC, and gNOESY) was used to define stemodiosides B3 and B4 as cucurbitacin steroidal glucosides. Thus stemodioside B3 is (24Z)-3, -(, -glucopyranosyloxy)-2,,20,27-trihydroxy-19-(10,9,)- abeo -10, -lanost-5,24-diene-11-one and stemodioside B4 is (23E)-3, -(, -glucopyranosyloxy)-2,,20,22,27-tetrahydroxy-19-(10,9,)- abeo -10, -lanost-5,23-diene-11-one. The approximate oral LD50s for stemodiosides B3 and B4 in mice were estimated to be 99 and 42 mg/kg body weight, respectively. Copyright © 2006 John Wiley & Sons, Ltd. [source] Electrospray ionization tandem mass spectrometry fragmentation of protonated flavone and flavonol aglycones: a re-examinationRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 2 2009Gonçalo C. Justino Flavonoids are important phytochemicals which have been intensively studied in the last decades in view of their antioxidant activity, which is of particular importance in the case of flavones and flavonols, that differ in a single 3-OH group. Mass spectrometry has been used to elucidate the structures of many types of flavonoids and their metabolites. The work we present here is focused on the electrospray ionization tandem mass spectrometry (ESI-MS/MS) analysis of flavone and flavonols aglycones. Their fragmentation mechanisms in the positive ion mode are described and compared with previously reported mechanisms. We analyzed flavonoid derivatives produced by reaction of the flavonoids with chemically synthesized hypohalous acids (HOCl, HOBr and HOI) and peroxynitrite, reactive species involved in the inflammatory response. All the proposed pathways have been analyzed using computational chemistry methods in order to seek for possible variations and establish the most plausible ones. We observed that the losses of one and two CO molecules can be useful in terms of antioxidant activity prediction. Losses of one and two C2H2O groups are also informative in terms of structure and activity predictions. The retro-Diels-Alder fragmentations, and subsequent neutral losses, were reviewed and, according to our calculations, the most plausible structures for the product ions were established. These fingerprints will be of great value for differentiating flavonoids from other compounds in complex biological mixtures and for a thorough structural identification of flavonoid aglycones and their invivo metabolites. Copyright © 2008 John Wiley & Sons, Ltd. [source] Gas-phase fragmentation study of novel synthetic 1,5-benzodiazepine derivatives using electrospray ionization tandem mass spectrometryRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 14 2008Mohamed Rida The fragmentation patterns of a series of three novel synthesized 3-hydroxy-4-phenyl-tetrahydro-1,5-benzodiazepin-2-ones (1,3), possessing the same backbone structure, were investigated using electrospray ionization mass spectrometry (ESI-MS) and tandem mass spectrometry (MS/MS) techniques. A simple methodology, based on the use of ESI (positive ion mode) and by increasing the declustering potential in the atmospheric pressure/vacuum interface, collision-induced dissociation (CID), was used to enhance the formation of the fragment ions. In general, the novel synthetic 1,5-benzodiazepine derivatives afforded, in the gas phase, both protonated and sodiated molecules. This led to the confirmation of the molecular masses and chemical structures of the studied compounds. Exact accurate masses were measured using a high-resolution ESI-quadrupole orthogonal time-of-flight (QqToF)-MS/MS hybrid mass spectrometer instrument. The breakdown routes of the protonated molecules were rationalized by conducting low-energy collision CID-MS/MS analyses (product ion- and precursor ion scans) using a conventional quadrupole-hexapole-quadrupole (QhQ) tandem mass spectrometer. All the observed major fragmentations for the 1,5-benzodiazepines occurred in the saturated seven-membered ring containing the nitrogen atoms. These formed a multitude of product ions by different breakdown routes. All the major fragmentations involved cleavages of the N -1,C -2 andC -3,C -4 bonds. These occurred with concomitant eliminations of glyoxal, benzene and ethyl formate, forming the product ion at m/z 119, which was observed in all the studied compounds. In addition, an unique simultaneous CID-MS/MS fragmentation was noticed for the 1,5-benzodiazepines 1 and 3, which occurred by a pathway dictated by the substituent located on the N -1-position. It was evident that the aromatic ring portion of the 1,5-benzodiazepines was resistant to CID-MS/MS fragmentation. Re-confirmation of the various geneses of the product ions was achieved by conducting a series of precursor ion scans. ESI-MS and CID-MS/MS analyses have thus proven to be a specific and very sensitive method for the structural identification of these novel 1,5-benzodiazepine derivatives. Copyright © 2008 John Wiley & Sons, Ltd. [source] Structural characterization of constituents with molecular diversity in fractions from Lysidice brevicalyx by liquid chromatography/diode-array detection/electrospray ionization tandem mass spectrometry and liquid chromatography/nuclear magnetic resonance,RAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 6 2008Jing Qu A combination of electrospray ionization tandem mass spectrometry with high-performance liquid chromatography (HPLC/ESI-MSn), and hyphenation of liquid chromatography to nuclear magnetic resonance spectroscopy (HPLC/NMR), have been extensively utilized for on-line analysis of natural products, analyzing metabolite and drug impurity. In our last paper, we reported an on-line analytical method for structural identification of trace alkaloids in the same class. However, the structural types of the constituents in plants were various, such as flavanoids, terpenoids and steroids. It is important to establish an effective analytical method for on-line structural identification of constituents with molecular diversity in extracts of plants. So, in the present study, the fragmentation patterns of some isolated stilbenes, phloroglucinols and flavanoids from Lysidice rhodostegia were investigated by ESI-MSn. Their fragmentation rules and UV characteristics are summarized, and the relationship between the spectral characteristics, rules and the structures is described. According to the fragmentation rules, NMR and UV spectral characteristics, 24 constituents of different types in the fractions from L. brevicalyx of the same genus were structurally characterized on the basis of HPLC/HRMS, HPLC-UV/ESI-MSn, HPLC/1H NMR and HPLC/1H- 1H COSY rapidly. Of these, six (10, 13, 14, 16, 17 and 23) are new compounds and all of them are reported from L. brevicalyx for the first time. The aim is to develop an effective analytical method for on-line structural identification of natural products with molecular diversity in plants, and to guide the rapid and direct isolation of novel compounds by chemical screening. Copyright © 2008 John Wiley & Sons, Ltd. [source] Use of high-performance liquid chromatography/electrospray ionization collision-induced dissociation mass spectrometry for structural identification of monohydroxylated progesteronesRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 23 2004Min-Jung Kang For the structural identification of monohydroxylated progesterones synthesized by microorganisms, a method was developed using a combination of high-performance liquid chromatography and electrospray ionization collision-induced dissociation mass spectrometry (HPLC/ESI-CIDMS). The retention times and MS/MS spectra of 11 different standards at 30,eV were collected and compared. The identification of D-ring-hydroxylated progesterones (15, -, 16, -, 17, - and 21-OH-P) using ESI-CIDMS was not possible. However, they were separated chromatographically using a 65:35 mixture of water and acetonitrile containing 0.5% acetic acid. The other hydroxylated progesterones (2, -, 6, -, 7, -, 9, -, 11, -, 11, -, and 19-OH-P) could be identified by comparison of eight fragments. The complete separation of 11 standards was achieved chromatographically. The developed assay was evaluated by the identification of monohydroxylated progesterones produced by CYP106A2 from Bacillus megaterium ATCC 13368. Copyright © 2004 John Wiley & Sons, Ltd. [source] Application of an efficient strategy based on MAE, HPLC-DAD-MS/MS and HSCCC for the rapid extraction, identification, separation and purification of flavonoids from Fructus Aurantii ImmaturusBIOMEDICAL CHROMATOGRAPHY, Issue 3 2010Chen Wang Abstract This study presents an efficient strategy based on microwave-assisted extraction (MAE), HPLC-DAD-MS/MS and high-speed counter-current chromatography (HSCCC) for the rapid extraction, identification, separation and purification of active components from the traditional Chinese medicine Fructus Aurantii Immaturus. An LC-DAD-MS/MS method was applied for the screening and structural identification of main components in crude extract, and five components were preliminarily identified as neoeriocitrin, narirutin, naringin, hesperidin and neohesperidin according to their UV and mass spectra. An efficient MAE method for the extraction of the three most abundant components (narirutin, naringin and neohesperidin) was optimized by the combination of univariate and multivariate approaches. The crude extract was then separated and purified by HSCCC and a total of 61.6 mg of narirutin, 207.3 mg of naringin and 159.5 mg of neohesperidin at high purities of 98.1, 97.2 and 99.5%, respectively, were obtained from 1.42 g of crude extract. The recoveries of these compounds were 86, 93 and 89%, respectively. Copyright © 2009 John Wiley & Sons, Ltd. [source] Conformational Analysis of R207910, a New Drug Candidate for the Treatment of Tuberculosis, by a Combined NMR and Molecular Modeling ApproachCHEMICAL BIOLOGY & DRUG DESIGN, Issue 2 2006Sandrine Gaurrand R207910 is an enantiomeric compound from a new class of antimycobacterial agents, the diarylquinolines [Science; 307:223 (2005)]. As enantiospecific interaction is required for biologic activity, we have undertaken a combined nuclear magnetic resonance and molecular modeling study to gain new insights into its conformation in solution and its absolute configuration. A conformational analysis using a Monte-Carlo method has been performed on each of the four possible stereomers of this compound leading to the identification of their most stable conformation. Additional ab initio calculation was performed with emphasis on the strength of the observed intramolecular hydrogen bond. Simultaneously, a complete structural identification has been carried out by a set of monodimensional and bidimensional 1H- 13C-NMR experiments. Determination of inter-proton distances has been achieved by a series of 1H- 1H ROESY NMR experiments with different mixing times followed by a volume quantification of the correlations peaks. These experimental data were compared with the theoretical distances obtained from the conformational analysis. The remarkable match shows that R207910 adopts one of the low-energy conformations predicted by molecular modeling and belongs to the (RS, SR) couple of diastereoisomers. A posteriori validation of our approach has been performed by X-ray structure determination that concluded for the RS configuration. [source] Water as a Building Block in Solid-State Acetonitrile,Pyrogallol[4]arene Assemblies: Structural InvestigationsCHEMISTRY - A EUROPEAN JOURNAL, Issue 29 2007Scott Abstract Under various conditions, water molecules dramatically affect a number of solid-state C -alkylpyrogallol[4]arene assemblies. In the absence of water, hydrogen-bonded hexameric capsules are formed for the C -butyl, pentyl, hexyl, and heptyl pyrogallol[4]arenes. Introduction of water to acetonitrile solutions containing C -propyl,C -octylpyrogallol[4]arenes resulted in the formation of markedly different bilayer structures and the structural identification of two new dimer-type motifs. [source] Determination of triclosan metabolites by using in-source fragmentation from high-performance liquid chromatography/negative atmospheric pressure chemical ionization ion trap mass spectrometryRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 13 2010Jian-lin Wu Triclosan is a widely used broad-spectrum antibacterial agent that acts by specifically inhibiting enoyl,acyl carrier protein reductase. An in vitro metabolic study of triclosan was performed by using Sprague-Dawley (SD) rat liver S9 and microsome, while the invivo metabolism was investigated on SD rats. Twelve metabolites were identified by using in-source fragmentation from high-performance liquid chromatography/negative atmospheric pressure chemical ionization ion trap mass spectrometry (HPLC/APCI-ITMS) analysis. Compared to electrospray ionization mass spectrometry (ESI-MS) and tandem mass spectrometry (MS/MS) that gave little fragmentation for triclosan and its metabolites, the in-source fragmentation under APCI provided intensive fragmentations for the structural identifications. The invitro metabolic rate of triclosan was quantitatively determined by using HPLC/ESI-ITMS with the monitoring of the selected triclosan molecular ion. The metabolism results indicated that glucuronidation and sulfonation were the major pathways of phase II metabolism and the hydroxylated products were the major phase I metabolites. Moreover, glucose, mercapturic acid and cysteine conjugates of triclosan were also observed in the urine samples of rats orally administrated with triclosan. Copyright © 2010 John Wiley & Sons, Ltd. [source] | ||||||||||