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Proton-transfer Reaction (proton-transfer + reaction)
Selected AbstractsTheoretical Study on Proton-Transfer Reaction of Intracellular Second-messenger 3,,5,-Cyclic NucleotideCHINESE JOURNAL OF CHEMISTRY, Issue 8 2008Ai-Hua ZHANG Abstract The gas-phase proton-transfer reaction mechanism of intracellular second-messenger 3,,5,-cyclic nucleotide (cAMPm) has been theoretically investigated at the B3LYP/6-31G, , level. One or two H2O molecules have been used to simulate the catalyst. It is found that H shift reaction between conformation Bm and conformation Dm of cAMPm involves a cyclic transition state with one or two water molecules as a shuttle. Furthermore, H shift reaction proceeds easily with the participation of two water molecules. The results provide evidence in theory to study proton-transfer reaction mechanism of related phosphodiesters. Our present calculations have rationalized all the possible reaction channels. [source] Ionization-Induced Proton Transfer in Model DNA Base Pairs: A Theoretical Study of the Radical Ions of the 7-Azaindole DimerCHEMPHYSCHEM, Issue 12 2004Hsing-Yin Chen Dr. Abstract Proton-transfer reactions of the radical anion and cation of the 7-Azaindole (7AI) dimer were investigated by means of density functional theory (DFT). The calculated results for the dimer anion and cation were very similar. Three equilibrium structures, which correspond to the non-proton-transferred (normal), the single-proton-transferred (SPT) and the double-proton-transferred (tautomeric) forms, were found. The transition states for proton-transfer reactions were also located. The calculations showed that the first proton-transfer reaction (normal,SPT) is exothermic and almost barrier-free; therefore, it should occur spontaneously in the period of a vibration. In contrast, the second proton-transfer reaction (SPT,tautomer) was found to be far less-probable in terms of reaction energy and barrier. Hence, it was concluded that both (7AI)2and (7AI)2exist in the SPT form. The conclusion was further confirmed by the calculated electron vertical detachment energy (VDE) of the SPT form of (7AI)2, 1.33 eV, which is very close to the experimental measurement of 1.35 eV. The calculated VDEs of the normal and tautomeric (7AI)2forms were too small compared to the experimental value. The proton transfer process was found to be multidimensional in nature involving not only proton motion but also intermolecular rocking motion. In addition, IR spectra were calculated and reported. The spectra of the three structures showed very different features and, therefore, can be considered as fingerprints for future experimental identifications. The implications of these results to biology and spectroscopy are also briefly discussed. [source] Sequence-dependent proton-transfer reaction in stacked GC pair III: The influence of proton transfer to conductivityINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 12 2010Yasuyuki Nakanishi Abstract We have computed current,voltage character of natural DNA and its proton-transferred structure by scattering theory based on density functional theory. The current is not observed if the electron path contains only hydrogen bonding such as one base pair. The current becomes larger if the electron path contains ,,, stacking molecule such as two base pairs. We also found that the conductivity of pseudo-ion pair (C+G,/G,C+), which is derived from proton-transfer reaction in CG/GC, differs from that of the original structure. On the other hand, the current changes dramatically if the electrode connects to guanine or cytosine, which can be explained by the difference of electron affinities. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2010 [source] Cation-Enhanced Deprotonation of Water by a Strong PhotobaseISRAEL JOURNAL OF CHEMISTRY, Issue 2 2009Noga Munitz We have used picosecond fluorescence spectroscopy to study the proton-dissociation dynamics of bulk water and H2O molecules solvating Mg2+ ions in aqueous solutions. We have analyzed the photo-initiated proton-transfer reaction to a photobase 6-aminoquinoline by the Collins-Kimball approach and have modeled the ensuing bimolecular reaction dynamics by the Smoluchowski equation with radiation boundary conditions. We have found the on-contact proton transfer rate to follow the Marcus free-energy relation for proton transfer and estimate by this rate-equilibrium correlation the considerable enhancement in the acidity of the water molecules solvating the Mg2+ ion. Our findings may be used in the study of metallo-enzymes such as carbonic anhydrases (CAs), which catalyze the reversible addition reaction of OH, to CO2 by increasing the reactivity of the zinc-bound water molecules by means of stabilizing the product of water dissociation, the OH, anion. [source] Quantitatively resolving mixtures of isobaric compounds using chemical ionization mass spectrometry by modulating the reactant ion compositionRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 16 2008E. C. Fortner Acrolein (C3H4O) and 1-butene (C4H8) can both be individually detected by proton transfer chemical ionization mass spectrometry (CI-MS). However, because these compounds are isobaric, mixtures of these two compounds cannot be resolved since both compounds react with H3O+ via a proton-transfer reaction to form a protonated molecule that is detected at a nominal mass-to-charge ratio of 57 (m/z 57). While both compounds react with H3O+ only acrolein reacts to any significant extent with H3O+(H2O). Recognizing that the electrical potential applied to a drift tube reaction mass spectrometer provides a simple and effective means for varying the relative intensity of the H3O+ and H3O+(H2O) reactant ions we have developed a method whereby we make use of this reactivity difference to resolve mixtures of these two compounds. We demonstrate a technique where the individual contributions of acrolein and 1-butene within a mixture can be quantitatively resolved by systematically changing the reagent ion from H3O+ to H3O+(H2O) through control of the electric potential applied to the drift tube reaction region of a proton transfer reaction mass spectrometer. Copyright © 2008 John Wiley & Sons, Ltd. [source] Ultrafast Relaxation Dynamics of the Excited States of 1-Amino- and 1-(N,N -Dimethylamino)-fluoren-9-onesCHEMPHYSCHEM, Issue 17 2009Mahendra Varne Abstract The dynamics of the excited states of 1-aminofluoren-9-one (1AF) and 1-(N,N -dimethylamino)-fluoren-9-one (1DMAF) are investigated by using steady-state absorption and fluorescence as well as subpicosecond time-resolved absorption spectroscopic techniques. Following photoexcitation of 1AF, which exists in the intramolecular hydrogen-bonded form in aprotic solvents, the excited-state intramolecular proton-transfer reaction is the only relaxation process observed in the excited singlet (S1) state. However, in protic solvents, the intramolecular hydrogen bond is disrupted in the excited state and an intermolecular hydrogen bond is formed with the solvent leading to reorganization of the hydrogen-bond network structure of the solvent. The latter takes place in the timescale of the process of solvation dynamics. In the case of 1DMAF, the main relaxation pathway for the locally excited singlet, S1(LE), or S1(ICT) state is the configurational relaxation, via nearly barrierless twisting of the dimethylamino group to form the twisted intramolecular charge-transfer, S1(TICT), state. A crossing between the excited-state and ground-state potential energy curves is responsible for the fast, radiationless deactivation and nonemissive character of the S1(TICT) state in polar solvents, both aprotic and protic. However, in viscous but strong hydrogen-bond-donating solvents, such as ethylene glycol and glycerol, crossing between the potential energy surfaces for the ground electronic state and the hydrogen-bonded complex formed between the S1(TICT) state and the solvent is possibly avoided and the hydrogen-bonded complex is weakly emissive. [source] Acid,Base Chemistry at the Ice Surface: Reverse Correlation Between Intrinsic Basicity and Proton-Transfer Efficiency to Ammonia and Methyl AminesCHEMPHYSCHEM, Issue 17 2007Seong-Chan Park Dr. Abstract Proton transfer from the hydronium ion to NH3, CH3NH2, and (CH3)2NH is examined at the surface of ice films at 60 K. The reactants and products are quantitatively monitored by the techniques of Cs+ reactive-ion scattering and low-energy sputtering. The proton-transfer reactions at the ice surface proceed only to a limited extent. The proton-transfer efficiency exhibits the order NH3>(CH3)NH2=(CH3)2NH, which opposes the basicity order of the amines in the gas phase or aqueous solution. Thermochemical analysis suggests that the energetics of the proton-transfer reaction is greatly altered at the ice surface from that in liquid water due to limited hydration. Water molecules constrained at the ice surface amplify the methyl substitution effect on the hydration efficiency of the amines and reverse the order of their proton-accepting abilities. [source] Ionization-Induced Proton Transfer in Model DNA Base Pairs: A Theoretical Study of the Radical Ions of the 7-Azaindole DimerCHEMPHYSCHEM, Issue 12 2004Hsing-Yin Chen Dr. Abstract Proton-transfer reactions of the radical anion and cation of the 7-Azaindole (7AI) dimer were investigated by means of density functional theory (DFT). The calculated results for the dimer anion and cation were very similar. Three equilibrium structures, which correspond to the non-proton-transferred (normal), the single-proton-transferred (SPT) and the double-proton-transferred (tautomeric) forms, were found. The transition states for proton-transfer reactions were also located. The calculations showed that the first proton-transfer reaction (normal,SPT) is exothermic and almost barrier-free; therefore, it should occur spontaneously in the period of a vibration. In contrast, the second proton-transfer reaction (SPT,tautomer) was found to be far less-probable in terms of reaction energy and barrier. Hence, it was concluded that both (7AI)2and (7AI)2exist in the SPT form. The conclusion was further confirmed by the calculated electron vertical detachment energy (VDE) of the SPT form of (7AI)2, 1.33 eV, which is very close to the experimental measurement of 1.35 eV. The calculated VDEs of the normal and tautomeric (7AI)2forms were too small compared to the experimental value. The proton transfer process was found to be multidimensional in nature involving not only proton motion but also intermolecular rocking motion. In addition, IR spectra were calculated and reported. The spectra of the three structures showed very different features and, therefore, can be considered as fingerprints for future experimental identifications. The implications of these results to biology and spectroscopy are also briefly discussed. [source] The Acidity of Brønsted CH Acids in DMSO , The Extreme Acidity of NonacyanocyclononatetraeneEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 24 2004Robert Vianello Abstract The gas-phase (GP) acidity of a large variety of CH organic acids is studied by a carefully selected B3LYP/6-311+G(2d,p)//B3LYP/6-31G(d) theoretical model. Acidities are mirrored by the proton affinities of the corresponding conjugate bases. A very good agreement with available experimental data is achieved. It is concluded that the model applied has a high predictive value and that theoretical PA(anion)GP values can be used instead of measured data in cases where experiments are not feasible or not performed. It is shown, employing the isodensity polarized continuum model (IPCM), that there is a good linear relationship between the enthalpies of the proton-transfer reactions in DMSO and the observed pKa(DMSO) values. This relation can be used in predicting the acidity of strong, neutral organic superacids. As an illustrative case, the acidity of cyclononatetraene-1,2,3,4,5,6,7,8,9-nonacarbonitrile ("nonacyanocyclononatetraene") is considered. It is conclusively shown that this compound should be a very potent superacid, as evidenced by its PA(anion)GP (260.0 kcal·mol,1) and pKa (,14.8). The origin of high acidity is identified as a very strong anionic resonance effect in the resulting conjugate base. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004) [source] Protein identification via ion-trap collision-induced dissociation and examination of low-mass product ionsJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 1 2008Jeremiah J. Bowers Abstract A whole-protein tandem mass spectrometry approach for protein identification based on precursor ion charge state concentration via ion/ion reactions, ion-trap collisional activation, ion/ion proton-transfer reactions involving the product ions, and mass analysis over a narrow m/z range (up to m/z 2000) is described and evaluated. The experiments were carried out with a commercially available electrospray ion-trap instrument that has been modified to allow for ion/ion reactions. Reaction conditions and the approach to searching protein databases were developed with the assumption that the resolving power of the mass analyzer is insufficient to distinguish charge states on the basis of the isotope spacings. Ions derived from several charge states of cytochrome c, myoglobin, ribonuclease A, and ubiquitin were used to evaluate the approach for protein identification and to develop a two-step procedure to database searching to optimize specificity. The approach developed with the model proteins was then applied to whole cell lysate fractions of Saccharomyces cerevisiae. The results are illustrated with examples of assignments made for three a priori unknown proteins, each selected randomly from a lysate fraction. Two of the three proteins were assigned to species present in the database, whereas one did not match well any database entry. The combination of the mass measurement and the product ion masses suggested the possibility for the oxidation of two methionine residues of a protein in the database. The examples show that this limited whole-protein characterization approach can provide insights that might otherwise be lacking with approaches based on complete enzymatic digestion. Copyright © 2007 John Wiley & Sons, Ltd. [source] Ionization-Induced Proton Transfer in Model DNA Base Pairs: A Theoretical Study of the Radical Ions of the 7-Azaindole DimerCHEMPHYSCHEM, Issue 12 2004Hsing-Yin Chen Dr. Abstract Proton-transfer reactions of the radical anion and cation of the 7-Azaindole (7AI) dimer were investigated by means of density functional theory (DFT). The calculated results for the dimer anion and cation were very similar. Three equilibrium structures, which correspond to the non-proton-transferred (normal), the single-proton-transferred (SPT) and the double-proton-transferred (tautomeric) forms, were found. The transition states for proton-transfer reactions were also located. The calculations showed that the first proton-transfer reaction (normal,SPT) is exothermic and almost barrier-free; therefore, it should occur spontaneously in the period of a vibration. In contrast, the second proton-transfer reaction (SPT,tautomer) was found to be far less-probable in terms of reaction energy and barrier. Hence, it was concluded that both (7AI)2and (7AI)2exist in the SPT form. The conclusion was further confirmed by the calculated electron vertical detachment energy (VDE) of the SPT form of (7AI)2, 1.33 eV, which is very close to the experimental measurement of 1.35 eV. The calculated VDEs of the normal and tautomeric (7AI)2forms were too small compared to the experimental value. The proton transfer process was found to be multidimensional in nature involving not only proton motion but also intermolecular rocking motion. In addition, IR spectra were calculated and reported. The spectra of the three structures showed very different features and, therefore, can be considered as fingerprints for future experimental identifications. The implications of these results to biology and spectroscopy are also briefly discussed. [source] | |||||||||||||||||||