Kinetic and mechanistic insight into the thermodynamic degradation of saxagliptin

The dipeptidyl peptidase-IV inhibitor saxagliptin (Onglyza) can undergo a thermodynamically favored cyclization to form the corresponding cyclic amidine. The kinetics and mechanism of this conversion were examined to develop a commercial synthesis that afforded saxagliptin with only trace levels of this key byproduct. Important findings of this work are the identification of a profound solvent effect and the determination of an autocatalytic pathway. Both of these phenomena result from transition structures involving proton transfer.     

A mechanistic insight into caspase-7 inhibition by BIR1-2 domains of XIAP and cIAP1

Previous studies failed to demonstrate any role for the BIR1 domain of the inhibitor of apoptosis proteins (IAPs) in inhibition of executioner caspases. In this study, XIAP-BIR1-2 and c-IAP1-BIR1-2 domains have been used to investigate the role of BIR1 in the inhibition of caspase-7. Kinetic analysis confirmed that caspase-7 was inhibited in an uncompetitive manner at lower concentrations of XIAP-BIR1-2, whereas the inhibition was switched to the mixed type mode at higher concentrations of the inhibitor. In contrast, cIAP1-BIR1-2 inhibited caspase-7 in a mixed type mode at all examined concentrations. These data suggest that the presence of BIR1 is essential for inhibition of caspase-7 by cIAP1. Far-UV CD and fluorescence spectroscopy experiments showed that despite similar secondary structures, XIAP-BIR1-2 and cIAP1-BIR1-2 have different biophysical properties. BIR1-2 domain of XIAP was found to be more flexible than cIAP1, which may be the reason behind differences in their kinetic properties.     

New insight into hydrogen bond-mediated electron transfer

<正>Electron transfer (ET) is one of the most fundamental processes in nature, biological systems, and optoelectronic devices. The in-depth ET investigations of synthetic materials are of great significance for the understanding of those occurring in natural systems. Mixed-valence (MV) compounds,consisting of two bridged redox motifs that are structurally identical but different in valence, provide an appealing     

Structural insight into RNA hairpin folding intermediates

Hairpins are a ubiquitous secondary structure motif in RNA molecules. Despite their simple structure, there is some debate over whether they fold in a two-state or multi-state manner. We have studied the folding of a small tetraloop hairpin using a serial version of replica exchange molecular dynamics on a distributed computing environment. On the basis of these simulations, we have identified a number of intermediates that are consistent with experimental results. We also find that folding is not simply the reverse of high-temperature unfolding and suggest that this may be a general feature of biomolecular folding.     

Electron-transfer oxidation properties of unsaturated fatty acids and mechanistic insight into lipoxygenases

Rate constants of photoinduced electron-transfer oxidation of unsaturated fatty acids with a series of singlet excited states of oxidants in acetonitrile at 298 K were examined and the resulting electron-transfer rate constants (k(et)) were evaluated in light of the free energy relationship of electron transfer to determine the one-electron oxidation potentials (E(ox)) of unsaturated fatty acids and the intrinsic barrier of electron transfer. The k(et) values of linoleic acid with a series of oxidants are the same as the corresponding k(et) values of methyl linoleate, linolenic acid, and arachidonic acid, leading to the same E(ox) value of linoleic acid, methyl linoleate, linolenic acid, and arachidonic acid (1.76 V vs SCE), which is significantly lower than that of oleic acid (2.03 V vs SCE) as indicated by the smaller k(et) values of oleic acid than those of other unsaturated fatty acids. The radical cation of linoleic acid produced in photoinduced electron transfer from linoleic acid to the singlet excited state of 10-methylacridinium ion as well as that of 9,10-dicyanoanthracene was detected by laser flash photolysis experiments. The apparent rate constant of deprotonation of the radical cation of linoleic acid was determined as 8.1 x 10(3) s(-1). In the presence of oxygen, the addition of oxygen to the deprotonated radical produces the peroxyl radical, which has successfully been detected by ESR. No thermal electron transfer or proton-coupled electron transfer has occurred from linoleic acid to a strong one-electron oxidant, Ru(bpy)3(3+) (bpy = 2,2'-bipyridine) or Fe(bpy)3(3+). The present results on the electron-transfer and proton-transfer properties of unsaturated fatty acids provide valuable mechanistic insight into lipoxygenases to clarify the proton-coupled electron-transfer process in the catalytic function.     

Reactivity and mechanistic insight into visible-light-induced aerobic cross-dehydrogenative coupling reaction by organophotocatalysts

With visible-light irradiation, a mild, simple, and efficient metal-free photocatalytic system for the facile construction of sp(3)-sp(3) C-C bonds between tertiary amines and activated C-H bonds has been achieved. Spectroscopic study and product analysis demonstrate for the first time that photoinduced electron transfer from N-aryl tetrahydroisoquinolines to eosin Y bis(tetrabutylammonium salt) (TBA-eosin Y) takes place to generate TBA-eosin Y radical anion, which can subsequently react with nucleophiles and molecular oxygen. More strikingly, electron spin resonance (ESR) measurements provide direct evidence for the formation of superoxide radical anions (O(2)(-.)) rather than singlet oxygen ((1)O(2)) during visible-light irradiation. This active species is therefore believed to be responsible for the large rate of acceleration of the aerobic photocatalytic reactions.     

Ethanol and water adsorption in methanol-derived ZIF-71

A room temperature method for synthesizing zeolitic imidizolate framework 71 (ZIF-71) is described. The methanol-based synthesis results in >95% yields (based on Zn) and produces crystals with 70% greater surface area than reported earlier. Ethanol uptake into the ZIF compares favorably with a recent modeling-based study. Water uptake was significantly higher than model predictions.     

Selectfluor: mechanistic insight and applications

The replacement of hydrogen atoms with fluorine substituents in organic substrates is of great interest in synthetic chemistry because of the strong electronegativity of fluorine and relatively small steric footprint of fluorine atoms. Many sources of nucleophilic fluorine are available for the derivatization of organic molecules under acidic, basic, and neutral conditions. However, electrophilic fluorination has historically required molecular fluorine, whose notorious toxicity and explosive tendencies limit its application in research. The necessity for an electrophilic fluorination reagent that is safe, stable, highly reactive, and amenable to industrial production as an alternative to very hazardous molecular fluorine was the inspiration for the discovery of selectfluor. This reagent is not only one of the most reactive electrophilic fluorinating reagents available, but it is also safe, nontoxic, and easy to handle. In this Review we document the many applications of selectfluor and discuss possible mechanistic pathways for its reaction.     

Additivity rule holds in the hydrogen transfer reactivity of unsaturated fatty acids with a peroxyl radical: mechanistic insight into lipoxygenase

A simple additivity rule holds in the hydrogen transfer reactivity of unsaturated fatty acids with cumylperoxyl radical, which is expressed by the additive contributions of the reactivity of active hydrogens from the 1,4-pentadiene subunit and those of the allylic subunit; the kinetic isotope effect on the hydrogen transfer reactions (KIE = 6.1) is significantly smaller than that observed for lipoxygenase (KIE = 81).     

Understanding the tetrazole ring cleavage reaction with hydrazines: Structural determination and mechanistic insight

A distinction in the behaviour of several hydrazines as N-nucleophiles in the recently developed one-pot method for pyrimidine core annulation via 1H-tetrazole ring cleavage was examined. The product structures, 2,3-diamino- or hydrazino derivatives of thieno[3,2-d]pyrimidin-4(3H)-ones, thieno[2,3-d]pyrimidin-4(3H)-ones and [1]benzofuro[3,2-d]pyrimidin-4(3H)-one, were elucidated based on NMR and single crystal X-ray analysis.     

Palladium catalysts for aerobic oxidative kinetic resolution of secondary alcohols based on mechanistic insight

The oxidative kinetic resolution of secondary alcohols has been accomplished using 1:1 complexes of PdCl(2) and N-heterocyclic carbenes. In these reactions, both achiral and chiral carbene ligands are used in conjunction with the chiral base (-)-sparteine. A general synthesis of 1:1 PdCl(2)-carbene complexes has been developed and is amenable to a wide range of carbene ligands. The potential of these complexes in aerobic oxidations is highlighted by the use of a chiral Pd(II) complex and the chiral base (-)-sparteine to enhance the kinetic resolution of a racemic alcohol. [reaction--see text]     

Structural and mechanistic insights into C-P bond hydrolysis by phosphonoacetate hydrolase

Bacteria have evolved pathways to metabolize phosphonates as a nutrient source for phosphorus. In Sinorhizobium meliloti 1021, 2-aminoethylphosphonate is catabolized to phosphonoacetate, which is converted to acetate and inorganic phosphate by phosphonoacetate hydrolase (PhnA). Here we present detailed biochemical and structural characterization of PhnA that provides insights into the mechanism of C-P bond cleavage. The 1.35?? resolution crystal structure reveals a catalytic core similar to those of alkaline phosphatases and nucleotide pyrophosphatases but with notable differences, such as a longer metal-metal distance. Detailed structure-guided analysis of active site residues and four additional cocrystal structures with phosphonoacetate substrate, acetate, phosphonoformate inhibitor, and a covalently bound transition state mimic provide insight into active site features that may facilitate cleavage of the C-P bond. These studies expand upon the array of reactions that can be catalyzed by enzymes of the alkaline phosphatase superfamily.     

Discovery of and mechanistic insight into a ligand-modulated palladium-catalyzed Wacker oxidation of styrenes using TBHP

We describe the discovery of a new N-heterocyclic carbene-modulated Pd catalyst for the Wacker oxidation that does not require molecular oxygen but instead uses TBHP as a reagent in this oxidation. The catalyst activity and selectivity for the oxidation of styrene derivatives to methyl ketones are among the best reported. Preliminary mechanistic studies of the catalytic system were performed and show that the origin of the carbonyl oxygen is TBHP and that the hydrogens in the product all originate from the starting olefin.     

Iridium-promoted deoxyglycoside synthesis: stereoselectivity and mechanistic insight

Herein, we devised a method for stereoselective O-glycosylation using an Ir(i)-catalyst which enables both hydroalkoxylation and nucleophilic substitution of glycals with varying substituents at the C3 position. In this transformation, 2-deoxy-α-O-glycosides were acquired when glycals equipped with a notoriously poor leaving group at C3 were used; in contrast 2,3-unsaturated-α-O-glycosides were produced from glycals that bear a good leaving group at C3. Mechanistic studies indicate that both reactions proceed via the directing mechanism, through which the acceptor coordinates to the Ir(i) metal in the α-face-coordinated Ir(i)-glycal π-complex and then attacks the glycal that contains the O-glycosidic bond in a syn-addition manner. This protocol exhibits good functional group tolerance and is exemplified with the preparation of a library of oligosaccharides in moderate to high yields and with excellent stereoselectivities.

Ir(i)-catalyzed α-selective O-glycosylation of glycals provided an access to both 2-deoxyglycosides and 2,3-unsaturated glycosides with a broad substrate scope. The underlying rationale of α-selectivity has been illustrated by the DFT study.     

An in-depth mechanistic insight into the redox reaction and degradation of aqueous Zn-MnO2 batteries

Rechargeable aqueous Zn/MnO₂ batteries raise massive research activities in recent years. However, both the working principle and the degradation mechanism of this battery chemistry are still under debate. Herein, we provide an in-depth electrochemical and structural investigation on this controversial issue based on α-MnO₂ crystalline nanowires. Mechanistic analysis substantiates a two-electron reaction pathway of Mn²⁺/Mn⁴⁺ redox couple from part of MnO₂ accompanying with a reversible precipitation/dissolution of flaky zinc sulfate hydroxide (ZSH) during the discharge/charge processes. The formation of the ZSH layer is double-edged, which passivates the deep dissolution of MnO₂ upon discharging, but promotes the electrochemical deposition kinetics of active MnO₂ upon charging. The cell degradation originates primarily from the corrosion failure of metallic zinc anode and the accumulation of irreversible ZnMn₂O₄ phases on the cathode. The addition of MnSO₄ to the electrolyte could afford supplementary capacity contribution via electro-oxidation of Mn²⁺. However, a high MnSO₄ concentration will expedite the cell failure by corroding the metallic zinc anodes. The present study will shed a fundamental insight on developing new strategies toward practically viable Zn/MnO₂ batteries.     

Structural insight into the glucokinase-ligands interactions. Molecular docking study

Glucokinase (GK) plays a key role in the regulation of hepatic glucose metabolism. Inactivation of GK is associated with diabetes, and an increase of its activity is linked to hypoglycemia. Possibility to regulate the GK activity using small chemical compounds as allosteric activators induces the scientific interest to the study of the activation mechanism and to the development of new allosteric glucokinase activators.Interaction of glucokinase with ligands is the first step of the complicated mechanism of regulation of the GK functioning. In this paper, we study the interaction of GK with native (glucose) and synthetic (allosteric activators) ligands using molecular docking method. Calculations demonstrate the ability of molecular docking programs to accurately reproduce crystallized ligand poses and conformations and to calculate a free energy of binding with satisfactory accuracy. Correlation between the free energy of binding and the bioactivity of activators is discussed. These results provide a new insight into protein–ligand interactions and can be used for the engineering of new activators.     

New mechanistic insight into electronically excited CO-NiO(100): a quantum dynamical analysis

In a recent study Redlich et al. [Redlich et al., Chem. Phys. Lett. 2006, 420, 110] measured the velocity distribution of CO molecules desorbing from a NiO(100) surface after irradiation with an ultraviolet (UV) laser pulse. Due to the complexity of the involved processes no experimental evidence on the excitation and desorption mechanism could be obtained. In recent ab initio studies Mehdaoui et al. [Mehdaoui et al., Phys. Rev. Lett. 2007, 98, 037601] have shown that a 5sigma --> 2pi* (a (3)Pi) like transition within the CO adsorbate is most likely the crucial excitation step in the CO-NiO(100) system. At first sight this seems unlikely, since the interaction of CO molecules with the NiO(100) surface is very weak (-0.30 eV) and the corresponding CO gas phase transition energy is about 1.5 eV higher than the laser pulse energy of 4.66 eV used in the experiment. In this work we give further insight into relevant electronically excited states and identify the desorption mechanism by analysing the dynamical processes after laser excitation by quantum dynamical wave packet simulations on the basis of three-dimensional (3D) ab initio potential energy surfaces. The results corroborate the so far discussed excitation mechanism, which proposes the formation of a genuine C-Ni bond as the driving force for photodesorption, as the crucial excitation step.