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Proton Transfer (proton + transfer)
Kinds of Proton Transfer Terms modified by Proton Transfer Selected AbstractsBis(dithiolene) Molybdenum Complex that Promotes Combined Coupled Electron,Proton Transfer and Oxygen Atom Transfer Reactions: A Water-Active Model of the Arsenite Oxidase Molybdenum CenterEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 22 2006Hideki Sugimoto Abstract Combined CEPT (coupled electron,proton transfer)/OAT (oxygen atom transfer) reactions were accomplished in (Bu4N)2[MoIVO(bdtCl2)2] (1) and (Bu4N)2[MoVIO2(bdtCl2)2] (2) complexes in aqueous media. The reaction mechanism of the CEPT reaction was analyzed electrochemically and the conversion of 1 to 2 was revealed to proceed by a two-proton two-electron oxidative process. The structural and reaction profiles provide a new model for the arsenite oxidase catalytic center. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006) [source] Ingredients Necessary for Proton Transfer in EnzymesISRAEL JOURNAL OF CHEMISTRY, Issue 2 2009Steve Scheiner The transfer of a proton across a hydrogen bond can be influenced by a number of factors, including H-bond length, intramolecular angles, and the presence of neighboring groups. The ability of different factors to push a proton across the H-bond is examined for a specific and very important pair of catalytic groups, Ser-195 and His-57, within the context of a serine proteinase enzyme. The influence of residue Asp-102 is considered for different charge states, as is the nature of the surrounding medium. Also examined are the perturbations introduced by the substrate and external ions and dipoles. [source] Proton Transfer on the Molecular Surface of Proteins and Model SystemsISRAEL JOURNAL OF CHEMISTRY, Issue 2 2009Ran Friedman Proton transfer (PT) reactions take place on the molecular surface of proteins, membranes, ionic polymers, and other molecules. The rates of the reactions can be followed experimentally, while the atomistic details can be elucidated by molecular modeling. This manuscript gives a brief overview of the use of computer simulations and molecular modeling, in conjuction with experiments, to study PT reactions on the surface of solvated molecules. An integrative approach is discussed, where molecular dynamics simulations are performed with a protein, and quantum-mechanics-based calculations are performed on a small molecule. The simulation results allow the identification of the necessary conditions that yield PT reactions on the molecular surface. The reactions are efficient when they involve a donor and acceptor located a few Ĺ apart and under the influence of a negative electrostatic field. In proton-pumping proteins, it is possible to identify such conditions a priori and locate proton-attracting antenna domains without the need to mutate each potential donor and acceptor. Based on density functional theory calculations, the arrangement of water molecules that interconnect the donor and acceptor moieties is suggested as the rate-limiting step for proton transfer on the molecular surface. [source] A Role for Internal Water Molecules in Proton Affinity Changes in the Schiff Base and Asp85 for One-way Proton Transfer in Bacteriorhodopsin,PHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 4 2008Joel E. Morgan Light-induced proton pumping in bacteriorhodospin is carried out through five proton transfer steps. We propose that the proton transfer to Asp85 from the Schiff base in the L-to-M transition is accompanied by the relocation of a water cluster on the cytoplasmic side of the Schiff base from a site close to the Schiff base in L to the Phe219-Thr46 region in M. The water cluster present in L, formed at 170 K, is more rigid than that at room temperature. This may be responsible for blocking the conversion of L to M at 170 K. In the photocycle at room temperature, this water cluster returns to the site close to the Schiff base in N, with a rigid structure similar to that of L at 170 K. The increase in the proton affinity of Asp85, which is a prerequisite for the one-way proton transfer in the M-to-N transition, is suggested to be facilitated by a structural change which disrupts interactions between Asp212 and the Schiff base, and between Asp212 and Arg82. We propose that this liberation of Asp212 is accompanied by a rearrangement of the structure of water molecules between Asp85 and Asp212, stabilizing the protonated Asp85 in M. [source] The Role of Solvent on the Mechanism of Proton Transfer to Hydride Complexes: The Case of the [W3PdS4H3(dmpe)3(CO)]+ Cubane ClusterCHEMISTRY - A EUROPEAN JOURNAL, Issue 5 2010Andrés Abstract The kinetics of reaction of the [W3PdS4H3(dmpe)3(CO)]+ hydride cluster (1+) with HCl has been measured in dichloromethane, and a second-order dependence with respect to the acid is found for the initial step. In the presence of added BF4, the second-order dependence is maintained, but there is a deceleration that becomes more evident as the acid concentration increases. DFT calculations indicate that these results can be rationalized on the basis of the mechanism previously proposed for the same reaction of the closely related [W3S4H3(dmpe)3]+ cluster, which involves parallel first- and second-order pathways in which the coordinated hydride interacts with one and two acid molecules, and ion pairing to BF4, hinders formation of dihydrogen bonded adducts able to evolve to the products of proton transfer. Additional DFT calculations are reported to understand the behavior of the cluster in neat acetonitrile and acetonitrile,water mixtures. The interaction of the HCl molecule with CH3CN is stronger than the WH,,,HCl dihydrogen bond and so the reaction pathways operating in dichloromethane become inefficient, in agreement with the lack of reaction between 1+ and HCl in neat acetonitrile. However, the attacking species in acetonitrile,water mixtures is the solvated proton, and DFT calculations indicate that the reaction can then go through pathways involving solvent attack to the W centers, while still maintaining the coordinated hydride, which is made possible by the capability of the cluster to undergo structural changes in its core. [source] Anion Receptors Containing -NH Binding Sites: Hydrogen-Bond Formation or Neat Proton Transfer?CHEMISTRY - A EUROPEAN JOURNAL, Issue 1 2005Valeria Amendola Dr. Abstract When the amide-containing receptor 1+ is in a solution of dimethyl sulfoxide (DMSO) in the presence of basic anions (CH3COO,, F,, H2PO4,), it undergoes deprotonation of the -NH fragment to give the corresponding zwitterion, which can be isolated as a crystalline solid. In the presence of less basic anions (Cl,, Br,, NO3,), 1+ establishes true hydrogen-bond interactions of decreasing intensity. The less acidic receptor 2+ undergoes neat proton transfer with only the more basic anions CH3COO, and F,, and establishes hydrogen-bond interactions with H2PO4,. An empirical criterion for discerning neutralisation and hydrogen bonding, based on UV/Vis and 1H NMR spectra, is proposed. [source] Low-Energy-Barrier Proton Transfer Induced by Electron Attachment to the Guanine,,,Cytosine Base PairCHEMPHYSCHEM, Issue 4 2010Anna Szyperska Abstract The photoelectron spectrum of the anion of the guanine,,,cytosine base apair (GC)., is recorded for the first time. The observed variation in the spectral peak-height ratios with the source conditions suggests the presence of two or more anionic isomers. Two maxima of the broad bands in the photoelectron spectrum were measured at about 1.9 and about 2.6 eV. These values are very well reproduced by the vertical detachment energies of the B3LYP/6-31++G(d,p) calculated low-energy anionic structures, which are 1) the Watson,Crick base-pair anion with proton transferred from N1 of guanine to N3 of cytosine, 2) its analogue in which the proton is transferred from N9 of guanine to N7 of guanine, and 3) the global minimum geometry, which is formed from the latter anion by rotation of guanine about the axis approximately defined by C2 of guanine and C4 of cytosine. Furthermore, a minor difference in the stabilities of the two lowest energy anions explains the experimentally observed source (temperature) dependence of the PES spectrum. A rational procedure, based on the chemistry involved in the formation of anionic dimers, which enables the low-energy anions populated in the photoelectron spectrum to be identified is proposed. In contrast to the alternative combinatorial approach, which in the studied case would lead to carrying out quantum chemical calculations for 2000,2500 structures, the procedure described here reduces the computational problem to only 15 geometries. [source] Proton Transfer in the Complex H3N,,,HCl Catalyzed by Encapsulation into a C60 CageCHEMPHYSCHEM, Issue 7 2009Fang Ma Dr. Abstract Caged up: In contrast to acid,base behavior in solution, single molecules of NH3 and HCl do not react to form the ion pair NH4+Cl, in isolation. Proton transfer occurs in the complex H3N,,,HCl inside the C60 cage, to form the ion pair NH4+Cl, under the catalytic action of C60 (see picture). We report proton transfer in the complex H3N,,,HCl to form the ion pair NH4+Cl,, which is favored inside the C60 cage according to quantum chemical calculations. The results show that the NH4+Cl,@C60 is stable with an interaction energy of ,2.78 kcal,mol,1. Compared with the complex H3N,,,HCl without proton transfer, it is found that the C60 cage plays the role of a catalyst for proton transfer. In NH4+Cl,@C60 a negative charge area in the C60 cage is near the cation NH4+ whereas a positive charge area is near the anion Cl,. Also, a confinement effect of the C60 cage is noticed, as the endohedral structure of NH4+Cl, is more compact than the structure of NH4+Cl, in the gas-phase complex. These findings indicate that the catalysis by the C60 cage comes from two effects: 1) electrostatic inducement between the C60 cage and endohedral molecules and 2) the confinement effect that compresses endohedral molecular structures inside the C60 cage. In the infrared spectrum, it is found that the confinement effect of the cage can cause large blue shifts of the N,H stretching vibrations in NH4+Cl,@C60 compared with those in the NH4+Cl,,,,H2O complex. [source] How Does a Membrane Protein Achieve a Vectorial Proton Transfer Via Water Molecules?CHEMPHYSCHEM, Issue 18 2008Steffen Wolf Abstract We present a detailed mechanism for the proton transfer from a protein-bound protonated water cluster to the bulk water directed by protein side chains in the membrane protein bacteriorhodopsin. We use a combined approach of time-resolved Fourier transform infrared spectroscopy, molecular dynamics simulations, and X-ray structure analysis to elucidate the functional role of a hydrogen bond between Ser193 and Glu204. These two residues seal the internal protonated water cluster from the bulk water and the protein surface. During the photocycle of bacteriorhodopsin, a transient protonation of Glu204 leads to a breaking of this hydrogen bond. This breaking opens the gate to the extracellular bulk water, leading to a subsequent proton release from the protonated water cluster. We show in detail how the protein achieves vectorial proton transfer via protonated water clusters in contrast to random proton transfer in liquid water. [source] Excited-State Double Proton Transfer in Model Base Pairs: The Stepwise Reaction on the Heterodimer of 7-Azaindole AnaloguesCHEMPHYSCHEM, Issue 2 2008Wan-Ting Hsieh Abstract A four fused-ring system 11-propyl-6H-indolo[2,3-b]quinoline (6,HIQ) is strategically designed and synthesized; it possesses a central moiety of 7-azaindole (7AI) and undergoes excited-state double proton transfer (ESDPT). Despite a barrierless type of ESDPT in the 6,HIQ dimer, femtosecond dynamics and a kinetic isotope effect provide indications for a stepwise ESDPT process in the 6,HIQ/7AI heterodimer, in which 6,HIQ (deuterated 6,HIQ) delivers the pyrrolyl proton (deuteron) to 7AI (deuterated 7AI) in less than 150 fs, forming an intermediate with a charge-transfer-like ion pair, followed by the transfer of a pyrrolyl proton (deuteron) from cation-like 7AI (deuterated 7AI) to the pyridinyl nitrogen of the anion-like 6,HIQ (deuterated 6,HIQ) in ,1.5±0.3 ps (3.5±0.3 ps). The barrier of second proton transfer is estimated to be 2.86 kcal,mol,1 for the 6,HIQ/7AI heterodimer. [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] Excited State Intramolecular Proton Transfer of New Diphenyl- ethylene Derivatives Bearing Imino Group: A Combination of Experimental and Theoretical InvestigationCHINESE JOURNAL OF CHEMISTRY, Issue 7 2010Fang Gao Abstract In this paper, we described the synthesis and characterization of new diphenylethylene bearing imino group. We concentrated particularly on the investigation of the possibility of the excited state intramolecular charge transfer (ESIPT) of the new dyes experimentally and theoretically. The absorption and fluorescence spectroscopy of the dyes were determined in various solvents. The results showed that the maximal absorption wavelength of 2-[(4,- N,N -dimethylamino-diphenylethylene-4-ylimino)methyl]phenol (C1) and 4-[(4,- N,N -dimethylamino-diphenylethylene-4-ylimino)methyl]phenol (C2) exhibited almost independence on the solvent polarity. While as contrast, the maximal fluorescence wavelength of the dyes showed somewhat dependence on the solvent polarity. In particular, C1 displayed well-separated dual fluorescence spectroscopy. The second fluorescence peak was characterized with an "abnormal" fluorescence emission wavelength in aprotic solvents with large Stokes shift (ca. 140 nm in THF), which was much more than normal Stokes shift (ca. 30 nm in THF). This emission spectroscopy could be assigned to ESIPT emission. On the other hand, the ESIPT fluorescence of C1 was much reduced or lost in the protic solvents. While, only normal fluorescence emission was detected in various solvents. Although the absorption maxima of C1 exhibited about 10 nm red-shift with respect to those of C2, the normal fluorescence maxima of C1 and C2 were almost identical in various solvents. These results suggested that C1 could undergo ESIPT, but C2 was not able to proceed ESIPT. The molecular geometry optimization of phototautomers in the ground electronic state (S0) was carried out with HF method (Hartree-Fock) and at DFT level (Density Functional Theory) using B3LYP both, while the CIS was employed to optimize the geometries of the first singlet excited state (S1) of the phototautomers of C1 and C2 respectively. The properties of the ground state and the excited state of the phototautomers of C1 and C2, including the geometrical parameter, the energy, the frontier orbits, the Mulliken charge and the dipole moment change were performed and compared completely. The data were analyzed further based on our experimental results. Furthermore, the absorption and fluorescence spectra were calculated in theory and compared with the measured ones. The rate constant of internal proton transfer (9.831×1011 s,1) of C1 was much lower than that of salicylidene methylamine (C3, 2.045×1015 s,1), which was a typical Schiff base compound and was well demonstrated to undergo ESIPT easily under photoexcitation. [source] Photoinduced Excited State Intramolecular Proton Transfer of New Schiff Base Derivatives with Extended Conjugated Chromophores: A Comprehensive Theoretical SurveyCHINESE JOURNAL OF CHEMISTRY, Issue 6 2010Qi Wang Abstract This paper presented comprehensive theoretical investigation of excited state intramolecular proton transfer (ESIPT) of four new large Schiff base derivatives with extended conjugated chromophores. The properties of the ground state and the excited state of phototautomers of C1 to C4 [C1: 2-(4,-nitro-stilbene-4-ylimino)methylphenol; C2: 2-(4,-cyano-stilbene-4-ylimino)methylphenol; C3: 2-(4,-methoxyl-stilbene-4-ylimino)methylphenol; C4: 2-(4,- N,N -diethylamino-stilbene-4-ylimino)methylphenol], which included geometrical parameter, energy, rate constant, frontier orbit, Mulliken charge, dipole moment change, were studied by DFT (density functional theory), CIS (configuration interaction singles-excitation), TDDFT (time-dependent DFT) methods to analyze the effects of chromophore part on the occurrence of ESIPT and the role of substituent groups. The structural parameter calculation showed that the shorter RHN and larger ROH from enol to enol* form, and less twisted configuration in the excited state implied that these molecules could undergo ESIPT as excitation. Stable transition states and a low energy barrier were observed for C1 to C4. This suggested that chromophore part increased some difficulty to undergo ESIPT for these molecules, while the possibility of occurrence of ESIPT was quite high. The negative ,E* (,9.808 and ,9.163 kJ/mol) of C1 and C2 and positive ,E* (0.599 and 1.029 kJ/mol) of C3 and C4 indicated that withdrawing substituent groups were favorable for the occurrence of ESIPT. The reaction rate constants of proton transfer of these compounds were calculated in the S0 and S1 states respectively, and the high rate constants of these compounds were observed at S1 state. C1 even reached at 1.45×1015 s,1 in the excited state, which is much closed to 2.05×1015 s,1 of the parent moiety (salicylidene methylamine). Electron-donating and electron-withdrawing substituent groups had different effects on the electron density distribution of frontier orbits and Mulliken charges of the atoms, resulting in different dipole moment changes in enol*,keto* process. These differences in turn suggested that C1 and C2 had more ability to undergo ESIPT than C3 and C4. The ultraviolet/visible absorption spectra, normal fluorescence emission spectra and ESIPT fluorescence emission spectra of these compounds were predicted in theory. [source] The Lifetimes of Pharaonis Phoborhodopsin Signaling States Depend on the Rates of Proton Transfers,Effects of Hydrostatic Pressure and Stopped Flow Experiments,PHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 4 2008Takashi Kikukawa Pharaonis phoborhodopsin (ppR), a negative phototaxis receptor of Natronomonas pharaonis, undergoes photocycle similar to the light-driven proton pump bacteriorhodopsin (BR), but the turnover rate is much slower due to much longer lifetimes of the M and O intermediates. The M decay was shown to become as fast as it is in BR in the L40T/F86D mutant. We examined the effects of hydrostatic pressure on the decay of these intermediates. For BR, pressure decelerated M decay but slightly affected O decay. In contrast, with ppR and with its L40T/F86D mutant, pressure slightly affected M decay but accelerated O decay. Clearly, the pressure-dependent factors for M and O decay are different in BR and ppR. In order to examine the deprotonation of Asp75 in unphotolyzed ppR we performed stopped flow experiments. The pH jump-induced deprotonation of Asp75 occurred with 60 ms, which is at least 20 times slower than deprotonation of the equivalent Asp85 in BR and about 10-fold faster than the O decay of ppR. These data suggest that proton transfer is slowed not only in the cytoplasmic channel but also in the extracellular channel of ppR and that the light-induced structural changes in the O intermediate of ppR additionally decrease this rate. [source] Proton Transfer on the Molecular Surface of Proteins and Model SystemsISRAEL JOURNAL OF CHEMISTRY, Issue 2 2009Ran Friedman Proton transfer (PT) reactions take place on the molecular surface of proteins, membranes, ionic polymers, and other molecules. The rates of the reactions can be followed experimentally, while the atomistic details can be elucidated by molecular modeling. This manuscript gives a brief overview of the use of computer simulations and molecular modeling, in conjuction with experiments, to study PT reactions on the surface of solvated molecules. An integrative approach is discussed, where molecular dynamics simulations are performed with a protein, and quantum-mechanics-based calculations are performed on a small molecule. The simulation results allow the identification of the necessary conditions that yield PT reactions on the molecular surface. The reactions are efficient when they involve a donor and acceptor located a few Ĺ apart and under the influence of a negative electrostatic field. In proton-pumping proteins, it is possible to identify such conditions a priori and locate proton-attracting antenna domains without the need to mutate each potential donor and acceptor. Based on density functional theory calculations, the arrangement of water molecules that interconnect the donor and acceptor moieties is suggested as the rate-limiting step for proton transfer on the molecular surface. [source] Supramolecular association in proton-transfer adducts containing benzamidinium cations.ACTA CRYSTALLOGRAPHICA SECTION C, Issue 6 2010Four organic salts, namely benzamidinidium orotate (2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylate) hemihydrate, C7H9N2+·C5H3N2O4,·0.5H2O (BenzamH+·Or,), (I), benzamidinium isoorotate (2,4-dioxo-1,2,3,4-tetrahydropyrimidine-5-carboxylate) trihydrate, C7H9N2+·C5H3N2O4,·3H2O (BenzamH+·Isor,), (II), benzamidinium diliturate (5-nitro-2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-olate) dihydrate, C7H9N2+·C4H2N3O5,·2H2O (BenzamH+·Dil,), (III), and benzamidinium 5-nitrouracilate (5-nitro-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-ide), C7H9N2+·C4H2N3O4, (BenzamH+·Nit,), (IV), have been synthesized by a reaction between benzamidine (benzenecarboximidamide or Benzam) and the appropriate carboxylic acid. Proton transfer occurs to the benzamidine imino N atom. In all four acid,base adducts, the asymmetric unit consists of one tautomeric aminooxo anion (Or,, Isor,, Dil, and Nit,) and one monoprotonated benzamidinium cation (BenzamH+), plus one-half (which lies across a twofold axis), three and two solvent water molecules in (I), (II) and (III), respectively. Due to the presence of protonated benzamidine, these acid,base complexes form supramolecular synthons characterized by N+,H...O, and N+,H...N, (±)-charge-assisted hydrogen bonds (CAHB). [source] Proton transfer versus nontransfer in compounds of the diazo-dye precursor 4-(phenyldiazenyl)aniline (aniline yellow) with strong organic acids: the 5-sulfosalicylate and the dichroic benzenesulfonate salts, and the 1:2 adduct with 3,5-dinitrobenzoic acidACTA CRYSTALLOGRAPHICA SECTION C, Issue 10 2009Graham Smith The structures of two 1:1 proton-transfer red,black dye compounds formed by reaction of aniline yellow [4-(phenyldiazenyl)aniline] with 5-sulfosalicylic acid and benzenesulfonic acid, and a 1:2 nontransfer adduct compound with 3,5-dinitrobenzoic acid have been determined at either 130 or 200,K. The compounds are 2-(4-aminophenyl)-1-phenylhydrazin-1-ium 3-carboxy-4-hydroxybenzenesulfonate methanol solvate, C12H12N3+·C7H5O6S,·CH3OH, (I), 2-(4-aminophenyl)-1-phenylhydrazin-1-ium 4-(phenyldiazenyl)anilinium bis(benzenesulfonate), 2C12H12N3+·2C6H5O3S,, (II), and 4-(phenyldiazenyl)aniline,3,5-dinitrobenzoic acid (1/2), C12H11N3·2C7H4N2O6, (III). In compound (I), the diazenyl rather than the aniline group of aniline yellow is protonated, and this group subsequently takes part in a primary hydrogen-bonding interaction with a sulfonate O-atom acceptor, producing overall a three-dimensional framework structure. A feature of the hydrogen bonding in (I) is a peripheral edge-on cation,anion association also involving aromatic C,H...O hydrogen bonds, giving a conjoint R12(6)R12(7)R21(4) motif. In the dichroic crystals of (II), one of the two aniline yellow species in the asymmetric unit is diazenyl-group protonated, while in the other the aniline group is protonated. Both of these groups form hydrogen bonds with sulfonate O-atom acceptors and these, together with other associations, give a one-dimensional chain structure. In compound (III), rather than proton transfer, there is preferential formation of a classic R22(8) cyclic head-to-head hydrogen-bonded carboxylic acid homodimer between the two 3,5-dinitrobenzoic acid molecules, which, in association with the aniline yellow molecule that is disordered across a crystallographic inversion centre, results in an overall two-dimensional ribbon structure. This work has shown the correlation between structure and observed colour in crystalline aniline yellow compounds, illustrated graphically in the dichroic benzenesulfonate compound. [source] Proton Transfer in the Complex H3N,,,HCl Catalyzed by Encapsulation into a C60 CageCHEMPHYSCHEM, Issue 7 2009Fang Ma Dr. Abstract Caged up: In contrast to acid,base behavior in solution, single molecules of NH3 and HCl do not react to form the ion pair NH4+Cl, in isolation. Proton transfer occurs in the complex H3N,,,HCl inside the C60 cage, to form the ion pair NH4+Cl, under the catalytic action of C60 (see picture). We report proton transfer in the complex H3N,,,HCl to form the ion pair NH4+Cl,, which is favored inside the C60 cage according to quantum chemical calculations. The results show that the NH4+Cl,@C60 is stable with an interaction energy of ,2.78 kcal,mol,1. Compared with the complex H3N,,,HCl without proton transfer, it is found that the C60 cage plays the role of a catalyst for proton transfer. In NH4+Cl,@C60 a negative charge area in the C60 cage is near the cation NH4+ whereas a positive charge area is near the anion Cl,. Also, a confinement effect of the C60 cage is noticed, as the endohedral structure of NH4+Cl, is more compact than the structure of NH4+Cl, in the gas-phase complex. These findings indicate that the catalysis by the C60 cage comes from two effects: 1) electrostatic inducement between the C60 cage and endohedral molecules and 2) the confinement effect that compresses endohedral molecular structures inside the C60 cage. In the infrared spectrum, it is found that the confinement effect of the cage can cause large blue shifts of the N,H stretching vibrations in NH4+Cl,@C60 compared with those in the NH4+Cl,,,,H2O complex. [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] Intramolecular proton transfer induced by divalent alkali earth metal cation in the gas stateINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 4 2003Hongqi Ai Abstract Interactions between divalent alkali earth metal (DAEM) ions M (MBe, Mg, Ca, Sr, Ba) and the second stable glycine conformer in the gas phase, which can transfer into the ground-state glycine-M2+ (except the glycine,Be2+) among each corresponding isomers when these divalent metal ions are bound, are studied at the hybrid three-parameter B3LYP level with three different basis sets. Proton transfers from the hydroxyl to the amino nitrogen of the glycine without energy barriers have been first observed in the gas phase in these glycine,M2+ systems. The interaction between the glycine and these DAEM ions except beryllium and magnesium ion only create an amino hydrogen pointing to the original hydroxyl due to their weaker interaction relative to those divalent transition metal (DTM) ion-bound glycine derivatives, being obviously different from that between the glycine and DTM ions, in which two amino hydrogens point to the original hydroxyl oxygen when these metal-chelated glycine derivatives are produced. The interaction energy between the glycine and divalent magnesium would be the boundary of one or two amino hydrogens pointing to the hydrogyl oxygen, i.e., the ,170.3 kcal/mol of binding energy is a critical point. Similar intramolecular proton transfer has also been predicted for those DTM ion-chelated glycine systems; however, that in the gas state has not been observed in the monovalent metal ion-coordinated glycine systems. The binding energy between some monovalent TM ion and the glycine is similar to that of the glycine,Ba2+, which has the lowest binding strength among these DAEM,ion chelated glycine complexes. The difference among them only lies in the larger electrostatic and polarized effects in the latter, which favor the stability of the zwitterionic glycine form in the gas phase. According to these observations, we predict that the zwitterionic glycine would exist in the field of two positive charges in the gas phase. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem 94: 205,214, 2003 [source] Reactivity Pattern in the Room-Temperature Activation of NH3 by the Main-Group Atomic Ions Ga+, Ge+, As+ and Se+EUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 10 2010Gregory K. Koyanagi Abstract The activation of ammonia by the main-group cations Ga+, Ge+, As+ and Se+ has been explored both experimentally and theoretically. ICP/SIFT tandem mass spectrometer measurements of room-temperature kinetics have revealed a substantial variation in rates and product distributions across the Periodic Table of Elements. The main features of the observed primary chemistry include H-atom elimination, ammonia addition and a cation-assisted proton transfer to yield NH4+ that is second order in ammonia. These observations are shown to be completely consistent with computed potential energy surfaces for the reactions of each of the four atomic cations. Dehydrogenation by the elimination of molecular hydrogen, not observed experimentally, is shown by the calculations to be inhibited by the presence of a kinetic barrier. [source] The Role of Amine,B(C6F5)3 Adducts in the Catalytic Reduction of Imines with H2: A Computational StudyEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 15 2009Timofei Privalov Abstract This study thoroughly examines the potential energy surfaces (PESs) of two possible mechanisms for reduction of imines by B(C6F5)3 and H2. The key reaction steps of the first catalytic mechanism, which is the focus of our study, are: (i) the uptake of H2 by a thermally activated amine,B(C6F5)3 species; (ii) proton transfer from the NH2+ moiety of [RNH2CH2R,]+[HB(C6F5)3], to the imine; (iii) nucleophillic attack of the C-center of the iminium ion by the BH, group. The potential energy barriers of the latter, as determined by calculating the evolution of the H-bonded complex of an imine and [RNH2CH2R,]+[HB(C6F5)3], in toluene, are around 10 kcal,mol,1 each. In the second mechanism, only imines serve as basic partners of B(C6F5)3 in the H2 activation, which affords an [RN(H)CHR,]+[HB(C6F5)3], ion pair; direct reduction then proceeds via nucleophilic attack of the C-center by the BH, in [RN(H)CHR,]+[HB(C6F5)3],. This route becomes catalytic when the product amine is released into the solvent and B(C6F5)3 is re-used for H2 activation. Upon taking into account the association energy of an amine,B(C6F5)3 adduct [,9.5 kcal,mol,1 for tBuN(H)CH2Ph and B(C6F5)3 in toluene], the potential energy barrier for H2 uptake by an imine and B(C6F5)3 increases to 14.5 kcal,mol,1. We report a somewhat lower potential energy barrier for H2 uptake by thermally activated amine,B(C6F5)3 adducts [12.7 kcal,mol,1 for the B-N adduct of tBuN(H)CH2Ph and B(C6F5)3 in toluene], although the difference between the two H2 activationbarriers is within the expected error of the computational method. Two catalytic routes are compared based on B3LYP-computed PESs in solvent (toluene).(© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009) [source] Kinetics of Bis(p -nitrophenyl)phosphate (BNPP) Hydrolysis Reactions with Trivalent Lanthanide Complexes of N -Hydroxyethyl(ethylenediamine)- N,N,,N, -triacetate (HEDTA),EUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 8 2009C. Allen Chang Abstract Kinetic studies of hydrolysis reactions of BNPP [sodium bis(p -nitrophenyl)phosphate] with trivalent lanthanide (Ln3+) complexes of HEDTA [HEDTA = N -hydroxyethyl(ethylenediamine)- N,N,,N, -triacetate] were performed at pH 6.96,11.34 and 25 °C by a spectrophotometric method and by HPLC analysis. The reaction rates increase with increasing atomic number of lanthanide and solution pH from PrHEDTA to EuHEDTA and then decrease for heavier LnHEDTA complexes. Plots of pseudo-first-order rate constants (kobs) vs. pH could be fitted to the equation kobs = kLnL(OH)[LnL]T/{1,+,exp[,2.303(pH,,,pKh)]}, where kLnL(OH) is the rate constant for the reaction of LnHEDTA(OH), with BNPP, Kh is the hydrolysis constant of LnHEDTA, and [LnL]T is the total concentration of LnHEDTA. The pKh values obtained by the kinetic method are in the range 8.2,10.3 and are similar to those measured by potentiometric methods. At [LnL]T = 10,70 mM and pH 10.5, most of the observed pseudo-first-order rate constants could be fitted to a simple saturation kinetic model, kobs = k1K[LnHEDTA(OH),]/{1 + K[LnHEDTA(OH),]}, where K is the equilibrium constant for the formation for LnHEDTA(OH),BNPP and is in the range 2,147 M,1. The k1 values are in the range 1.12,×,10,5,2.71,×,10,3 s,1. The kobs data for TbHEDTA and HoHEDTA were fitted to a quadratic equation. It was observed that the dinuclear species are more reactive. ESI mass spectrometry confirmed that the reaction between BNPP and EuHEDTA is a simple hydrolysis but not a transesterification, presumably because the three inner-sphere coordinated water molecules are far away from the coordinated hydroxyethyl group. Hydrolysis is likely to occur by proton transfer from one inner-sphere coordinated water molecule to the deprotonated ethyl oxide group followed by nucleophilic attack of the resulting hydroxide ion on the bonded BNPP anion.(© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009) [source] Bis(dithiolene) Molybdenum Complex that Promotes Combined Coupled Electron,Proton Transfer and Oxygen Atom Transfer Reactions: A Water-Active Model of the Arsenite Oxidase Molybdenum CenterEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 22 2006Hideki Sugimoto Abstract Combined CEPT (coupled electron,proton transfer)/OAT (oxygen atom transfer) reactions were accomplished in (Bu4N)2[MoIVO(bdtCl2)2] (1) and (Bu4N)2[MoVIO2(bdtCl2)2] (2) complexes in aqueous media. The reaction mechanism of the CEPT reaction was analyzed electrochemically and the conversion of 1 to 2 was revealed to proceed by a two-proton two-electron oxidative process. The structural and reaction profiles provide a new model for the arsenite oxidase catalytic center. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006) [source] The Mechanism of the Stetter Reaction , A DFT StudyEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 33 2008Kirsty J. Hawkes Abstract On the basis of Breslow's mechanism for benzoin condensation, a model asymmetric Stetter reaction has been investigated using DFT methods. In contrast to the concerted benzoin condensation, after formation of the Breslow intermediate the Stetter reaction is found to be a two-step process in which the rate-determining C,C coupling of the Breslow intermediate and the Michael acceptor precedes final proton transfer. In addition, the enolamine is found to play a significant role in the stereochemistry of the product, with the energy difference between stereoisomers of this intermediate reflected throughout the remainder of the reaction sequence. Consequently, electronic and steric control of the stereochemistry of this intermediate should directly enhance the ee values of the product. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008) [source] The Mechanism of Hydrolysis of Aryl Ether Derivatives of3-HydroxymethyltriazenesEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 10 2005Emília Carvalho Abstract 1-Aryl-3-aryloxymethyl-3-methyltriazenes hydrolyse to the corresponding anilines and phenols by specific-acid-catalysed, general-acid-catalysed and pH-independent mechanisms. All compounds studied exhibit specific- and general acid catalysis, though for 5a general acid catalysis was not observed below a pH of approximately 4, while for compounds 5e,f, such catalysis was absent above a pH of approximately 5. The pH-independent pathway is observed only for those compounds, 5d,f, that contain good aryloxy nucleofugic groups. The specific-acid-catalysed pathway is supported by a solvent deuterium isotope effect (SDIE) of 0.64, consistent with a mechanism involving protonation of the substrate followed by rate-determining unimolecular decomposition of the protonated species. The kH+ values gave rise to a Hammett , value of ,0.93, reflecting the competing effect of the substituents on the protonation of the substrate and the cleavage of the aryl ether. Correlation of kH+ with the pKa of the phenol leaving group affords a ,lg of 0.3. Decomposition of the protonated intermediate proceeds via a triazenyliminium ion that can be trapped by methanol. The general-acid-catalysed process exhibits an SDIE of 1.43 and Hammett , values of 0.49, 0.84 and 1.0 for reactions catalysed by chloroacetic, formic and acetic acids, respectively. Correlation of kA with the pKa of the acid gave Brřnsted , values that diminish from 0.6 for O -aryl systems that are poor nucleofuges (5a,b) to 0.2 for the best nucleofuge (5f), reflecting the different extents of proton transfer required to expel each phenol. Compounds containing powerful nucleofuges exhibit a pH-independent reaction that has an SDIE of 1.1, a Hammett , value of 3.4 and a Brřnsted ,lg value of 1.4. These imply a mechanism involving displacement of the aryloxide leaving group to form a triazenyliminium ion intermediate that again was trapped as a methyl ether. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005) [source] A Combined Theoretical and Experimental Research Project into the Aminolysis of ,-Lactam Antibiotics: The Importance of Bifunctional CatalysisEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 21 2003Natalia Díaz Abstract This paper reports the results of experimental work on the aminolysis of penicillin (6-APA) and monobactam (aztreonam) antibiotics by propylamine or ethanolamine. In general, aztreonam is slightly more reactive than 6-APA, despite the common assumption that the amide bond should be less activated in monobactams. Intriguingly, when ethanolamine acts as the nucleophile, the corresponding rate law has a kinetic term proportional to [RNH2][RNH3+]. To complement the experimental observations, the rate-determining free energy barriers in aqueous solution for various mechanistic pathways were computed by standard quantum chemical methodologies. From previous theoretical work it was assumed that the aminolysis of ,-lactams proceeds through mechanisms in which either a water molecule or a second amine molecule may act as bifunctional catalysts, assisting proton transfer from the attacking amine molecule to the leaving amino group. The energy barriers as computed have moderate values (ca. 26,34 kcal·mol,1) and reproduce most of the experimentally observed kinetic trends. Furthermore, the calculations predict that positively charged ethanolamine molecules can act as bifunctional catalysts as well, thus explaining the presence of the kinetic term proportional to [RNH2][RNH3+] in the rate law. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003) [source] Assignment of the [4Fe-4S] clusters of Ech hydrogenase from Methanosarcina barkeri to individual subunits via the characterization of site-directed mutantsFEBS JOURNAL, Issue 18 2005Lucia Forzi Ech hydrogenase from Methanosarcina barkeri is a member of a distinct group of membrane-bound [NiFe] hydrogenases with sequence similarity to energy-conserving NADH:quinone oxidoreductase (complex I). The sequence of the enzyme predicts the binding of three [4Fe-4S] clusters, one by subunit EchC and two by subunit EchF. Previous studies had shown that two of these clusters could be fully reduced under 105 Pa of H2 at pH 7 giving rise to two distinct S˝ electron paramagnetic resonance (EPR) signals, designated as the g = 1.89 and the g = 1.92 signal. Redox titrations at different pH values demonstrated that these two clusters had a pH-dependent midpoint potential indicating a function in ion pumping. To assign these signals to the subunits of the enzyme a set of M. barkeri mutants was generated in which seven of eight conserved cysteine residues in EchF were individually replaced by serine. EPR spectra recorded from the isolated mutant enzymes revealed a strong reduction or complete loss of the g = 1.92 signal whereas the g = 1.89 signal was still detectable as the major EPR signal in five mutant enzymes. It is concluded that the cluster giving rise to the g = 1.89 signal is the proximal cluster located in EchC and that the g = 1.92 signal results from one of the clusters of subunit EchF. The pH-dependence of these two [4Fe-4S] clusters suggests that they simultaneously mediate electron and proton transfer and thus could be an essential part of the proton-translocating machinery. [source] Escherichia coli cyclophilin B binds a highly distorted form of trans -prolyl peptide isomerFEBS JOURNAL, Issue 18 2004Michiko Konno Cyclophilins facilitate the peptidyl-prolyl isomerization of a trans -isomer to a cis -isomer in the refolding process of unfolded proteins to recover the natural folding state with cis -proline conformation. To date, only short peptides with a cis -form proline have been observed in complexes of human and Escherichia coli proteins of cyclophilin A, which is present in cytoplasm. The crystal structures analyzed in this study show two complexes in which peptides having a trans -form proline, i.e. succinyl-Ala- trans -Pro-Ala- p -nitroanilide and acetyl-Ala-Ala- trans -Pro-Ala-amidomethylcoumarin, are bound on a K163T mutant of Escherichia coli cyclophilin B, the preprotein of which has a signal sequence. Comparison with cis -form peptides bound to cyclophilin A reveals that in any case the proline ring is inserted into the hydrophobic pocket and a hydrogen bond between CO of Pro and N,2 of Arg is formed to fix the peptide. On the other hand, in the cis -isomer, the formation of two hydrogen bonds of NH and CO of Ala preceding Pro with the protein fixes the peptide, whereas in the trans -isomer formation of a hydrogen bond between CO preceding Ala-Pro and His47 N,2 via a mediating water molecule allows the large distortion in the orientation of Ala of Ala-Pro. Although loss of double bond character of the amide bond of Ala-Pro is essential to the isomerization pathway occurring by rotating around its bond, these peptides have forms impossible to undergo proton transfer from the guanidyl group of Arg to the prolyl N atom, which induces loss of double bond character. [source] Functional analysis of disease-causing mutations in human galactokinaseFEBS JOURNAL, Issue 8 2003David J. Timson Galactokinase (EC 2.7.1.6) catalyzes the first committed step in the catabolism of galactose. The sugar is phosphorylated at position 1 at the expense of ATP. Lack of fully functional galactokinase is one cause of the inherited disease galactosemia, the main clinical manifestation of which is early onset cataracts. Human galactokinase (GALK1) was expressed in and purified from Escherichia coli. The recombinant enzyme was both soluble and active. Product inhibition studies showed that the most likely kinetic mechanism of the enzyme was an ordered ternary complex one in which ATP is the first substrate to bind. The lack of a solvent kinetic isotope effect suggests that proton transfer is unlikely to be involved in the rate determining step of catalysis. Ten mutations that are known to cause galactosemia were constructed and expressed in E. coli. Of these, five (P28T, V32M, G36R, T288M and A384P) were insoluble following induction and could not be studied further. Four of the remainder (H44Y, R68C, G346S and G349S) were all less active than the wild-type enzyme. One mutant (A198V) had kinetic properties that were essentially wild-type. These results are discussed both in terms of galactokinase structure-function relationships and how these functional changes may relate to the causes of galactosemia. [source] | ||||||||||||||||||||||||||||||||||||||||