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Model Molecules (model + molecule)
Selected AbstractsDetermination of binding sites in carboplatin-bound cytochrome c using electrospray ionization mass spectrometry and tandem mass spectrometryJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 8 2005Gaosheng Yang Abstract Interaction of carboplatin with cytochrome c (Cyt. c) has been investigated by electrospray ionization mass spectrometry (ESI-MS) and tandem mass spectrometry (MS/MS). ESI-MS studies revealed that the ring-opened adducts of carboplatin with Cyt. c were formed in the stoichiometric ratio of 1 : 1 and 2 : 1 at pH 5.0 and 37 °C and in the stoichiometric ratio of 1 : 1 only at pH 7.0 and 37 °C. It was also found that Cyt. c could be cleaved by carboplatin at pH 2.5 and 50 °C. The cleaved fragments of Cyt. c were determined by ESI-MS and MS/MS analysis to be Glu66,Met80, Ac-Gly01,Met65, Glu66,Glu104, Ac-Gly01,Met80 and Ile81,Glu104. The carboplatin prefers to anchor to Met65 first, then to Met80. To further confirm the binding site of Met, AcMet-Gly was used as the model molecule to investigate its interaction with carboplatin and its hydrolysis reaction. On the basis of species detected during the reaction monitored by ESI-MS, a possible pathway of the cleavage reaction was proposed. Copyright © 2005 John Wiley & Sons, Ltd. [source] Surface-enhanced Raman spectroscopy with ultraviolet excitationJOURNAL OF RAMAN SPECTROSCOPY, Issue 6-7 2005Xu-Feng Lin Abstract Surface-enhanced Raman scattering (SERS) spectroscopy excited with a UV laser was successfully developed and the UV,SER spectra of various adsorbates, including pyridine and SCN,, on different transition metal electrodes were obtained. The experimental requirements for obtaining UV,SERS in an electrochemical system are given. The surface enhancement factor of a roughened Rh electrode covered with thiocyanate as a model molecule was estimated to be about two orders of magnitude in the UV region, consistent with our preliminary theoretical calculation based on the electromagnetic model. The investigation of SERS in the UV region will improve the understanding of the SERS enhancement mechanism and broaden the research field of SERS in areas such as surface science and the life sciences. Copyright © 2005 John Wiley & Sons, Ltd. [source] Synthesis of a New Macromonomer from 2-(Dimethylamino)ethyl Methacrylate Bearing 1-(Isopropenylphenyl)-1,1-dimethylmethyl Isocyanate GroupMACROMOLECULAR CHEMISTRY AND PHYSICS, Issue 5 2004Cyril Boyer Abstract Summary: The telomerization of 2-(dimethylamino)ethyl methacrylate (DMAEMA) with 2-mercaptoethanol in acetonitrile shows that the telogen can react with the monomer by nucleophilic addition. It is to say that the tertiary amino group leads to nucleophilic addition rather than telomerization. The oligomers thus obtained were functionalized with 1-(isopropenylphenyl)-1,1-dimethylmethyl isocyanate (TMI) in anhydrous toluene to afford macromonomers. These macromonomers were copolymerized with styrene and the r1, r2 ratio was determined according to Jaacks and Macret's methods. It was thereby demonstrated that the r1 value for this type of monomer is close to zero. Structure of the model molecule. [source] Racemization of the gastrointestinal antisecretory chiral drug esomeprazole magnesium via the pyramidal inversion mechanism: A theoretical studyCHIRALITY, Issue 9 2010Hili Marom Abstract The pyramidal inversion mechanisms of the 6-methoxy and the 5-methoxy tautomers of (S)-omeprazole were studied, employing ab initio and DFT methods. The conformational space of the model molecule (S)-2-[(3-methyl-2-pyridinyl)methyl]sulfinyl-1H -benzimidazole was calculated, with respect to rotations around single bonds, at the B3LYP/6-311G(d,p) level. All of the resulting conformations were used as starting points for full optimizations of (S)-omeprazole, at B3LYP/6-31G(d), B3LYP/6-311G(d,p), B3LYP/6-311++G(d,p), B3LYP/6-311G(2df,2pd), MP2/6-31G(d), and MP2/6-311G(d,p) levels. Four distinct pathways were found for enantiomerization via the pyramidal inversion mechanism for each of the tautomers of (S)-omeprazole. Each transition state, in which the sulfur, the oxygen and the two carbon atoms connected directly to the sulfur are in one plane, connects two diastereomeric minima. The enantiomerization is completed by free rotation around the sulfur,methylene bond, and around the methylene,pyridine ring bond. The effective Gibbs' free energy barrier for racemization ,G of the two tautomers of (S)-omeprazole are 39.8 kcal/mol (5-methoxy tautomer) and 40.0 kcal/mol (6-methoxy tautomer), indicating that the enantiomers of omeprazole are stable at room temperature (in the gas phase). The 5-methoxy tautomer of (S)-omeprazole was found to be slightly more stable than the 6-methoxy tautomer, in the gas phase. The energy barrier (,G,) for the(S,M) (S,P) diastereomerization of (S)-omeprazole due to the rotation around the pyridine chiral axis was very low, 5.8 kcal/mole at B3LYP/6-311G(d,p). Chirality 2010. © 2010 Wiley-Liss, Inc. [source] CE with electrochemical detection for investigation of label-free recognition of amino acid amides by guanine-rich DNA aptamersELECTROPHORESIS, Issue 17 2007Tao Li Abstract In this work, we report a simple and effective investigation into adaptive interactions between guanine-rich DNA aptamers and amino acid amides by CE with electrochemical (EC) detection. Argininamide (Arm) and tyrosinamide (Tym) were chosen as model molecules. On a copper electrode, Arm generated a good EC signal in 60 mM NaOH at 0.7 V (vs Ag/AgCl), while Tym was detected well on a platinum electrode at 1.3 V in 20 mM phosphate of pH 7.0. Based on their EC properties, the ligands themselves were used as indicators for the adaptive interactions investigated by CE-EC, making any step of labeling and/or modification of aptamers with indicators exempted. Hydrophilic ionic liquid was used as an additive in running buffer of CE to improve the sensitivity of Arm detection, whereas the additive was not used for Tym detection due to its negative effect. Two guanine-rich DNA aptamers were used for molecular recognition of Arm and Tym. When the aptamers were incubated with ligands, they bound the model molecules with high affinity and specificity, reflected by obvious decreases in the signals of ligands but no changes in those of the control molecules. However, the ligands were hardly affected by the control ssDNAs after incubation. The results revealed the specific recognition of Arm and Tym by the aptamers. The mechanisms for binding model molecules by aptamers were discussed. Not as expected, these aptamers were not to form the G-quartets, which were generally responsible for binding the ligands when the guanine-rich aptamers were used. [source] Adapted DAX-8 fractionation method for dissolved organic matter (DOM) from soils: development, calibration with test components and application to contrasting soil solutionsEUROPEAN JOURNAL OF SOIL SCIENCE, Issue 6 2009F. Amery Summary Most methods to fractionate natural dissolved organic matter (DOM) rely on sorption of acidified DOM samples onto XAD-8 or DAX-8 resin. Procedural differences among methods are large and their interpretation is limited because there is a lack of calibration with DOM model molecules. An automated column-based DOM fractionation method was set up for 10-ml DOM samples, dividing DOM into hydrophilic (HPI), hydrophobic acid (HPOA) and hydrophobic neutral (HPON) fractions. Fifteen DOM model components were tested in isolation and in combination. Three reference DOM samples of the International Humic Substances Society were included to facilitate comparison with other methods. Aliphatic low-molecular-weight acids (LMWAs) and carbohydrates were classified as HPI DOM, but some LMWAs showed also a partial HPO character. Aromatic LMWAs and polyphenols partitioned in the HPOA fraction, menadione (quinone) and geraniol (terpenoid) in HPON DOM. Molecules with log Kow > 0.5 had negligible HPI fractions. The HPO molecules except geraniol had specific UV absorbance (SUVA, measure for aromaticity) >3 litres g,1 cm,1 while HPI molecules had SUVA values <3 litres g,1 cm,1. Distributions of DOM from eight soils ranged from 31 to 72% HPI, 25 to 46% HPOA and 2 to 28% HPON of total dissolved organic carbon. The SUVA of the HPI DOM was consistently smaller compared with the HPOA DOM. The SUVA of the natural DOM samples was not explained statistically by fractionation and the variation coefficient of SUVA among samples was not reduced by fractionation. Hence, fractionation did not reduce the variability in this DOM property, which casts some doubts on the practical role of DOM fractionation in predicting DOM properties. [source] Quantum chemical study of penicillin: Reactions after acylationINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 10 2007Rui Li Abstract The density functional theory methods were used on the model molecules of penicillin to determine the possible reactions after their acylation on ,-lactamase, and the results were compared with sulbactam we have studied. The results show that, the acylated-enzyme tetrahedral intermediate can evolves with opening of ,-lactam ring as well as the thiazole ring; the thiazole ring-open products may be formed via ,-lactam ring-open product or from tetrahedral intermediate directly. Those products, in imine or enamine form, can tautomerize via hydrogen migration. In virtue of the water-assisted, their energy barriers are obviously reduced. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007 [source] Impact of ketone and amino on the inner shell of guanineJOURNAL OF SYNCHROTRON RADIATION, Issue 4 2009Quan Zhu Removal of the functional groups of guanine, i.e. ketone and amino, one by one produces model molecules of hypoxanthine, 2-aminopurine and unsubstituted purine. The impact of the ketone and amino moieties on guanine is revealed using their atomic-site-based inner-shell electronic properties and spectra. A density functional theory based model has been employed to study the model molecules. Electronic properties, such as Hirshfeld charges and inner-shell chemical shift, are found to be both site-dependent and moiety-dependent. The site-based inner-shell chemical shift of the species exhibits a simple linear correlation, although certain similarities among the model molecules regroup the species into two pairs of purine and 2-aminopurine, as well as hypoxanthine and guanine. [source] Structural analysis of secondary ions by post-source decay in time-of-flight secondary ion mass spectrometryRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 4 2006David Touboul Tandem mass spectrometry measurements have been achieved using time-of-flight secondary ion mass spectrometry (TOF-SIMS) and a post source decay (PSD)-like method. The performance of the method has been demonstrated on model molecules with well-known fragmentation pathways. Several lipids have been fragmented including the phosphocholine ion, phosphatidylcholines, cholesterol and vitamin E. Pure samples were analyzed, and the results compared with those obtained with the same compounds on a quadrupole-TOF hybrid mass spectrometer. Then, the structures of some lipids which are currently observed in the TOF-SIMS imaging of mammalian tissue sections were verified. Copyright © 2006 John Wiley & Sons, Ltd. [source] Boryl-substituted 1-silacyclobutenes.APPLIED ORGANOMETALLIC CHEMISTRY, Issue 1 2007Formation, molecular structure Abstract The 1,2-hydroboration of the chloro(hexyn-1-yl)- (1a) and chloro(phenylethyn-1-yl)diphenylsilanes (1b) with 9-borabicyclo[3.3.1]nonane afforded selectively the alkenylsilanes 2a, b, in which the boryl and the silyl groups are linked to the same olefinic carbon atom. In case of 2a, treatment with phenylethynyl lithium gave a mixture of the alkyn-1-ylborate 3a and the alkenyl(phenylethynyl)diphenylsilanes 4a. In the case of 2b, only the alkyn-1-ylsilane 4b was identified as an intermediate. Both 4a, b slowly rearranged by intramolecular 1,1-vinylboration into the silacyclobutenes 5a, b. The intermediates were characterized by 1H, 11B, 13C and 29Si NMR spectroscopy in solution, and the molecular structure of the 1-silacyclobutene 5a was determined by X-ray analysis. The gas phase geometries of model molecules corresponding to 5a were optimized by MO calculations using DFT methods [B3LYP/6-311 + G(d,p) level of theory], found to be in reasonable agreement with the results of the crystal structure determination, and NMR parameters were calculated at the same level of theory. Copyright © 2006 John Wiley & Sons, Ltd. [source] | ||||||||||