Combined quantum mechanics/molecular mechanics study on the reversible isomerization of glucose and fructose catalyzed by Pyrococcus furiosus phosphoglucose isomerase

Phosphoglucose isomerase (PGI), which catalyzes the reversible interconversion of glucose 6-phosphate (G6P) and fructose 6-phosphate (F6P), is represented by two evolutionarily distinct protein families. One is a conventional type in eubacteria, eukaryotes, and a few archaea, where the active sites contain no metal ions and reactions proceed via the cis-enediol intermediate mechanism. The second type, found recently in euryarchaeota species, belongs to metalloenzymes, and controversies exist over whether the catalyzed isomerization occurs via the cis-enediol intermediate mechanism or a hydride shift mechanism. We studied the reversible interconversion of the open-chain form G6P and F6P catalyzed by the metal-containing Pyrococcus furiosus PGI by performing QM(B3LYP)/MM single-point optimizations and QM(PM3)/MM molecular dynamics simulations. A zwitterion intermediate-based mechanism, which involves both proton and hydride transfers, has been put forward. The presence of the key zwitterionic intermediate in this mechanism can effectively reconcile the controversial mechanisms and rationalize the enzymatic reaction. Computations show that the overall isomerization process is quite facile, both dynamically and thermodynamically. The crucial roles of conserved residues have been elucidated on the basis of computations on their alanine mutants. In particular, Tyr152 pushes the H1 transfer through a hydride-shift mechanism and dominates the stereochemistry selectivity of the hydrogen transfer. The rest of the conserved residues basically maintain the substrate in the near-attack reactive conformation and mediate the proton transfer. Although Zn(2+) is not directly involved in the reaction, the metal ion as a structural anchor constructs a hydrogen bond wire to connect the substrate to the outer region, providing a potential channel for hydrogen exchange between the substrate and solvent.     

On the mechanisms of oxidation of organic sulfides by H2O2 in aqueous solutions

The mechanism of oxidation of organic sulfides in aqueous solutions by hydrogen peroxide was investigated via ab initio calculations. Specifically, two reactions, hydrogen transfer of hydrogen peroxide to form water oxide and the oxidation of dimethyl sulfide (DMS) by hydrogen peroxide to form dimethyl sulfoxide, were studied as models of these processes in general. Solvent effects are included both via including explicitly water molecules and via the polarizable continuum model. The former was found to have a much more significant effect than the latter. When explicit water molecules are included, a mechanism different from those proposed in the literature was found. Specific interactions including hydrogen bonding with 2-3 water molecules can provide enough stabilization for the charge separation of the activation complex. The energy barrier of the oxidation of DMS by hydrogen peroxide was estimated to be 12.7 kcal/mol, within the experimental range of the oxidation of analogous compounds (10-20 kcal/mol). The major reaction coordinates of the reaction are the breaking of the O-O bond of H2O2 and the formation of the S-O bond, the transfer of hydrogen to the distal oxygen of hydrogen peroxide occurring after the system has passed the transition state. Reaction barriers of the hydrogen transfer of H2O2 are an average of 10 kcal/mol or higher than the reaction barriers of the oxidation of DMS. Therefore, a two-step oxidation mechanism in which, first, the transfer of a hydrogen atom occurs to form water oxide and, second, the transfer of oxygen to the substrate occurs is unlikely to be correct. Our proposed oxidation mechanism does not suggest a pH dependence of oxidation rate within a moderate range around neutral pH (i.e., under conditions in which hydronium and hydroxide ions do not participate directly in the reaction), and it agrees with experimental observations over moderate pH values. Also, without including a protonated solvent molecule, it has activation energies that correspond to measured activation energies.     

Interactions of oxidative radicals with N-phosphoryl dipeptide derivatives

The interactions of oxidative radicals (Br2 , HO etc.) with N-phosphoryl dipeptide derivatives (NDM-TrpOMe and NDT-MetOMe) have been investigated by using pulse radiolysis at different pH values. Ithas been found that Br2 and HO radicals oxidize the Met-site and Trp-site in the dipeptide derivatives via formation of the three-electron-bonded intermediate and indolyl radical simultaneously. Then the intramolecular electron transfer along the peptide backbone occurs. The rate constants of electron transfer, k, have been determined and the reaction mechanism has been deduced.     

Proton transfer in nanoconfined polar solvents. II. Adiabatic proton transfer dynamics

The reaction dynamics for a model phenol-amine proton transfer system in a confined methyl chloride solvent have been simulated by mixed quantum-classical molecular dynamics. In this approach, the proton vibration is treated quantum mechanically (and adiabatically), while the rest of the system is described classically. Nonequilibrium trajectories are used to determine the proton transfer reaction rate constant. The reaction complex and methyl chloride solvent are confined in a smooth, hydrophobic spherical cavity, and radii of 10, 12, and 15 A have been considered. The effects of the cavity radius and the heavy atom (hydrogen bond) distance on the reaction dynamics are considered, and the mechanism of the proton transfer is examined in detail by analysis of the trajectories.     

Solvent effects in the geometric reorganization of an oxo-molybdenum(V) system

We have previously postulated a serine gated electron transfer hypothesis (Inorg. Chem, 2002, 41, 1281-1291) to possibly be involved in gating electron transfer between the Mo(V) and Mo(IV) states. In this study we explored the effect of solvent dielectric upon the rate and mechanism of isomerization of an oxo-Mo(V) core in attempt to understand the effect of solvent polarity to the isomerization reaction. To this end, the data suggests that there may be significant entropic contributions to the reorganization of metal center as a function of the local dielectric constant. Furthermore, we note that there is a change in the observed rate as well as the mechanism of the geometric rearrangement when it is examined in polar and non-polar environments. More specifically, in low dielectric media, the reaction proceeds either via a fast dissociation which is then followed by a twist mechanism or by a dissociation that is synchronized with the twist mechanism.     

Photoaddition of water and alcohols to the anthracene moiety of 9-(2'-hydroxyphenyl)anthracene via formal excited state intramolecular proton transfer

The title compound undergoes efficient photoaddition of a molecule of a hydroxylic solvent (H(2)O, MeOH, (Me)(2)CHOH) across the 9- and 10-positions of the anthracene moiety to give isolable triphenylmethanol or triphenylmethyl ether type products. The reaction is believed to proceed via a mechanism involving water-mediated formal excited state intramolecular proton transfer (ESIPT) from the phenolic OH to the 10-position of the anthracene ring, generating an o-quinone methide intermediate that is observable by nanosecond laser flash photolysis, and is trappable with nucleophiles. A "water-relay" mechanism for proton transfer seems plausible but cannot be proven directly with the data available. Irradiation in deuterated solvents led to incorporation of one deuterium atom at the methylene position in the photoaddition product, and partial deuterium exchange of the 10-position of recovered starting material, consistent with the proposed formal excited state proton transfer mechanism. The deuterium exchange and photoaddition reach maximum quantum efficiency at approximately 5 M water (in CH(3)CN or CH(3)OH), with no reaction observed in the absence of a hydroxylic solvent, demonstrating the sensitivity of this type of ESIPT to solvent composition.     

Theoretical modeling study for the phosphonylation mechanisms of the catalytic triad of acetylcholinesterase by sarin

Potential energy surfaces for the process of phosphonylation of the catalytic triad of acetylcholinesterase by sarin have been explored at the B3LYP/6-311G(d,p) level of theory through a computational study. It is concluded that the phosphonylation process involves a critical addition-elimination mechanism. The first nucleophilic addition process is the rate-determining step. The following elimination process of the fluoride ion comprises a composite reaction that includes several steps, and it occurs rapidly by comparison with the rate-determining step. The mobility characteristics of histidine play an important role in the reaction. A double proton-transfer mechanism is proposed for the catalytic triad during the phosphonylation process of sarin on AChE. The effect of aqueous solvation has been considered via the polarizable continuum model (PCM). One concludes that the energy barriers are generally lowered in solvent, compared to the gas-phase reactions.     

Synthesis of CuTCNQ/Au Microrods by Galvanic Replacement of Semiconducting Phase I CuTCNQ with KAuBr(4) in Aqueous Medium

The spontaneous reaction between microrods of an organic semiconductor molecule, copper 7,7,8,8-tetracyanoquinodimethane (CuTCNQ) with [AuBr(4)](-) ions in an aqueous environment is reported. The reaction is found to be redox in nature which proceeds via a complex galvanic replacement mechanism, wherein the surface of the CuTCNQ microrods is replaced with metallic gold nanoparticles. Unlike previous reactions reported in acetonitrile, the galvanic replacement reaction in aqueous solution proceeds via an entirely different reaction mechanism, wherein a cyclical reaction mechanism involving continuous regeneration of CuTCNQ consumed during the galvanic replacement reaction occurs in parallel with the galvanic replacement reaction. This results in the driving force of the galvanic replacement reaction in aqueous medium being largely dependent on the availability of [AuBr(4)](-) ions during the reaction. Therefore, this study highlights the importance of the choice of an appropriate solvent during galvanic replacement reactions, which can significantly impact upon the reaction mechanism. The reaction progress with respect to different gold salt concentration was monitored using Fourier transform infrared (FT-IR), Raman, and X-ray photoelectron spectroscopy (XPS), as well as XRD and EDX analysis, and SEM imaging. The CuTCNQ/Au nanocomposites were also investigated for their potential photocatalytic properties, wherein the destruction of the organic dye, Congo red, in a simulated solar light environment was found to be largely dependent on the degree of gold nanoparticle surface coverage. The approach reported here opens up new possibilities of decorating metal-organic charge transfer complexes with a host of metals, leading to potentially novel applications in catalysis and sensing.     

A Theoretical Investigation on N7(H)→N9(H)Tautomerization of Isolated and Monohydrated 2,6-Dithiopurine Combined with IPCM Solvent Model

The tautomerization reaction mechanism has been reported between N7(H) and N9(H) of isolated and monohydrated 2,6‐dithiopurine using B3LYP/6‐311+G(d,p). The isodensity polarized continuum model (IPCM) in the self‐consistent reaction field (SCRF) method is employed to account for the solvent effect of water on the tautomerization reaction activation energies. The results show that the two pathways P(1) (via the carbene intermediate I1) and P(2) (via the sp³‐hybrid intermediate I2) are found in intramolecular proton transfer, and each pathway is composed by two primary steps. The calculated activation energy barriers of the rate‐determining steps in isolated 2,6‐dithiopurine N7(H)→N9(H) tautomerism are 308.2 and 220.0 kJ·mol^?1 in the two pathways, respectively. Interestingly, in one‐water molecule catalyst, it dramatically lowers the N7(H)→N9(H) energy barriers by the concerted double proton transfer mechanism in P(1), favoring the formation of 2,6‐dithiopurine N9(H). However, the single proton transfer mechanism assisted with out‐of‐plane water in the first step of P(2) increases the activation energy barrier from 220.0 to 232.3 kJ·mol^?1, while the second step is the out‐of‐plane concerted double proton transfer mechanism, indicating that they will be less preferable for proton transfer. Additionally, the results also show that all the pathways are put into the aqueous solution, and the activation energy barriers have no significant changes. Therefore, the long‐range electrostatic effect of bulk solvent has no significant impact on proton transfer reactions and the interaction with explicit water molecules will significantly influence proton transfer reactions.     

Theoretical studies on the intramolecular hydrogen bond and tautomerism of 8-mercaptoquinoline in the gaseous phase and in solution using modern DFT methods

A theoretical quantum chemical study of the intramolecular hydrogen bonding interactions in 8-mercaptoquinoline has been carried out. Special attention has been paid to the rotation of S-H bond and intramolecular proton-transfer reactions. Therewith, the B3LYP/6-311++G(d,p), B3LYP/6-31+G(2d,2p), MPW1K/6-311++G(d,p), MPW1K/6-31+G(2d,2p), BH&HLYP/6-311++G(d,p), and G96LYP/6-311++G(d,p) methods have been used. By means of the Onsager and PCM reaction field methods, the effects of solvent on hydrogen-bond energies, conformational equilibria, rotational barriers, and tautomerism in aqueous solution have been studied. These simulations were done at the MPW1K/6-311++G(d,p) and B3LYP/6-311++G(d,p) levels. Natural-bond orbital analysis has been performed to study the intramolecular hydrogen bond (IHB) in the gaseous phase and in aqueous medium. The stability of forms under consideration in solution does not coincide with that in the gaseous phase, underlining a great importance of the electrostatic influence of solvent. Double-proton transfer in the prototropic tautomerization of 8-mercaptoquinoline, one water molecule complex in the gaseous phase and in solution, has been systematically studied. The double-proton transfer occurs concertedly and synchronously. The water-assisted tautomerization is kinetically less, but thermodynamically more favorable, compared to that of the single-proton transfer. As in the case with single-proton transfer, for water-assisted reaction, the tautomerization energies and barrier heights decrease with the increase in dielectric constant, which implies faster and more complete tautomerization of 8-mercaptoquinoline in a polar solvent.     

A way to avoid using precious metals: the application of high-surface activated carbon for the synthesis of isoindoles via the Diels-Alder reaction of 2H-pyran-2-ones

The application of activated carbon (Darco KB) for the acceleration and direction of the transformation of various 2H-pyran-2-ones with N-substituted maleimides toward isoindole derivatives through the reaction sequence cycloaddition/elimination/dehydrogenation is described. In this reaction, the catalyst mainly influences the dehydrogenation step, which is essential to avoid the formation of bicyclo[2.2.2]octenes as the other possible products. We found that the combination of Darco KB, as the metal-free catalyst, and decalin, as the solvent in a closed vessel, represents the most successful conditions. A comparison of the effect of various dehydrogenation catalysts and reaction conditions is also presented. In addition, we have proven that the aromatization occurs via a hydrogen transfer from the cyclohexadiene intermediate to the maleimide derivative (therefore producing succinimides). This transfer is facilitated by the active surface of the heterogeneous carbon-based catalyst.     

Investigation of the pathway for inter-copper electron transfer in peptidylglycine alpha-amidating monooxygenase

Peptidylglycine alpha-amidating monooxygenase catalyzes the oxidative cleavage of glycine extended peptides at their terminus. In the course of the reaction, there is a requisite long-range electron transfer between the two copper centers (CuH and CuM) located in the hydroxylating domain. This communication presents data that argue against the participation of the extended peptide backbone of substrate in the long-range electron transfer. We propose that electron transfer occurs via the bulk solvent that separates CuH from CuM.     

Theoretical study on formation of thioesters via O-to-S acyl transfer

Peptide thioester preparation via intramolecular O-to-S acyl transfer is a recently developed method for protein chemical synthesis through Fmoc chemistry. Theoretical calculations have been carried out to study the mechanism for the formation of thioesters via O-to-S acyl transfer. It is found that the O-to-S acyl transfer occurs via an anionic stepwise mechanism in which the cleavage of the C-O bond is the rate-limiting step. The side reaction of hydrolysis also proceeds through an anionic stepwise process, and its rate-limiting step is the attack of the hydroxide ion on the carbonyl carbon. Increase of the chain length between the ester O atom and the S atom can increase the energy barrier of the O-to-S acyl transfer. On the other hand, substituents at the α-position of the ester can reduce the energy barrier.     

Natural phenolic compounds in the reaction with a nitrogen-centered radical in an aprotic solvent

Kinetics and mechanism of the reaction of vegetable phenols (PhOH) with 2,2′-diphenyl-1-picrylhydrazyl radical (DPPH?) in a polar aprotic solvent, dimethyl sulfoxide, were studied. The reaction of natural phenols with DPPH? in dimethyl sulfoxide occurs in two stages. In the first stage, a proton-coupled electron transfer (PCET) occurs from a PhOH molecule to DPPH? to give primary transformation products, phenoxyl radicals (PhO?) and diphenyl hydrazine (DPPH–H), and in the second, the hydrazyl radical is consumed in the reaction with PhO? transformation products, enolized dimers, which is confirmed by NMR spectroscopy. A relationship was revealed between the antiradical activity of phenols in the reaction with DPPH? (ln k) and the ionization potential of the phenolates being formed.     

煤与废塑料共液化中氢转移的示踪试验研究

采用放射性同位素3H标记的四氢萘溶剂进行了先锋褐煤与低密度聚乙烯（LDPE）的共液化示踪试验,并考察了钼灰（FAMo）和Fe2O3+S催化剂的影响。应用液体闪烁计数器测量了各液化产物中的放射性活度,以研究煤与废塑料共液化中的氢转移。结果表明：在先锋褐煤与LDPE塑料共液化反应的初始阶段,存在着四氢萘溶剂的供氢作用,而且这种供氢作用不受催化剂的影响,只是热力作用的结果。使用加氢蒽油（HAO）和四氢萘（THN）溶剂混和物作为共液化溶剂时,先锋褐煤与LDPE共液化反应初期的溶剂供氢还存在着竞争转移,其主要取决于溶剂的脱氢能力。     

水杨酸激发态质子转移反应及其溶剂效应的理论研究

用AMI和INDO/CI方法对水杨酸的激发态质子转移反应进行了理论研究,求得反应的位能曲线、势垒和过渡态,对有关化合物的吸收和荧光光谱进行了理论指认,计算与实验结果符合较好。对光化学反应机理和应用前景进行了讨论,最后以乙醚作为氢键溶剂的例子研究了影响水杨酸激发态质子转移反应的溶剂效应。     

Mechanism of the hydrogen transfer from the OH group to oxygen-centered radicals: proton-coupled electron-transfer versus radical hydrogen abstraction

High-level ab initio electronic structure calculations have been carried out with respect to the intermolecular hydrogen-transfer reaction HCOOH+.OH-->HCOO.+H(2)O and the intramolecular hydrogen-transfer reaction .OOCH2OH-->HOOCH(2)O.. In both cases we found that the hydrogen atom transfer can take place via two different transition structures. The lowest energy transition structure involves a proton transfer coupled to an electron transfer from the ROH species to the radical, whereas the higher energy transition structure corresponds to the conventional radical hydrogen atom abstraction. An analysis of the atomic spin population, computed within the framework of the topological theory of atoms in molecules, suggests that the triplet repulsion between the unpaired electrons located on the oxygen atoms that undergo hydrogen exchange must be much higher in the transition structure for the radical hydrogen abstraction than that for the proton-coupled electron-transfer mechanism. It is suggested that, in the gas phase, hydrogen atom transfer from the OH group to oxygen-centered radicals occurs by the proton-coupled electron-transfer mechanism when this pathway is accessible.     

Mechanism of the Morita-Baylis-Hillman reaction: a computational investigation

Accurate calculations are presented on the mechanism of the MBH reaction, focusing on the reaction between methyl acrylate and benzaldehyde, catalyzed by a tertiary amine. We address the mechanism under protic solvent-free conditions, but also consider how the mechanism and rate-limiting step change in the presence of alcohols. We have carefully calibrated the DFT method used in the calculations by carrying out high-level G3MP2 calculations on a model system. All of our calculations also treat the effect of solvent, described as a dielectric continuum. In the absence of protic solvent, we predict that deprotonation of the alpha-position is the rate-determining step and occurs through a cyclic transition state, with proton transfer to a hemiacetal alkoxide formed by addition of a second equivalent of aldehyde to the intermediate alkoxide. As first suggested by McQuade, this mechanism explains the observed second-order kinetics with respect to aldehyde concentration in the absence of protic solvent. In contrast, in the presence of methanol, we find a slightly lower energy pathway, in which the alcohol serves as a shuttle to transfer the proton from carbon to oxygen. Overall, the barrier to reaction for the latter mechanism is of 24.6 kcal/mol with respect to reactants at the B3LYP level of theory. The relative energy for the addition transition state of the amine-acrylate betaine adduct to the aldehyde is much lower, at 16.0 kcal/mol relative to reactants, so C-C bond formation should not be rate-limiting, except perhaps for some aliphatic aldehydes or imines. We discuss the implications of this mechanism for the design of asymmetric versions of the MBH reaction, given the overwhelming importance of the proton-transfer step.     

Charge transfer complexing in the course of triplet state quenching of carbocyanine dyes by nitroxyl radical

Quenching of triplet states of carbocyanine dyes by nitroxyl radical has been investigated by the flash photolysis method. Quenching of triplet state carbocyanine dyes with one polymethyne chain occurs via enhanced intersystem crossing on exchange interaction with the radical. Quenching of triplet state carbocyanine dyes with two polymethyne chains occurs via partial charge transfer in the collision complex with the radical. In the second case, an increase in the dielectric constant of the solvent leads to an increase of the rate of quenching. In high polarity solvents (propanol, methanol) complete electron transfer from dye triplet state to radical occurs. Kinetic and spectral characteristics of a new dye radical (Dye.⁺) are reported.     

Carbene Formation or Reduction of the Diazo Functional Group? An Unexpected Solvent-Dependent Reactivity of Cyclic Diazo Imides

The control of the reactivity of diazo compounds is commonly achieved by the choice of a suitable catalyst, e.g. via stabilization of singlet carbenes or radical intermediates. Herein, we report on the light-promoted reactivity of cyclic diazo imides with thiols, where the choice of solvent results in two fundamentally different reaction pathways. In dichloromethane (DCM), a carbene is formed initially and engages in a cascade C−H functionalization/thiolation reaction to deliver indane-fused pyrrolidines in good to excellent yields. When switching to acetonitrile solvent, the carbene pathway is shut down and an unusual reduction of the diazo compound occurs under otherwise identical reaction conditions, where the aryl thiol acts as reductant. A combined set of experimental and computational studies was carried out to obtain mechanistic understanding and to support that indane formation proceeds via the insertion of a triplet carbene, while the reduction of diazo imides proceeds via an electron transfer process.