Establishing the mechanism of Rh-catalysed activation of O2 by H2

Reductive activation of O(2) by H(2) with rhodium terpyridine complexes in H(2)O and CH(3)CN is described and the mechanism is fully elucidated. The rhodium complex extracts electrons from H(2) and reductively activates O(2) to form a peroxo active intermediate. This intermediate is able to oxidise triphenyl phosphine to triphenyl phosphine oxide. A model system constructed in CH(3)CN provides isolable analogues of catalytic intermediates in H(2)O, allowing a detailed look at each step in the catalytic cycle.     

The mechanism of H2 activation by (amino)carbenes

We have computationally investigated the mechanism of the H(2) activation reaction by (amino)carbenes compounds. Describing the electronic activity taking place during the reaction through the Reaction Electronic Flux, it has been possible to elucidate the mechanism of the hydrogen activation process and assign the energetic cost associated to every chemical event that drives the process along the reaction coordinate; this is crucial information to rationalize the reported experimental results. It has been observed that the substituent effect may induce early charge-transfer phenomena that increases the energy barrier and lowers the exothermicity of the reaction. Reversibility of the process is discussed in light of specific interactions defining the components of the reverse activation energy.     

Mathematical modeling of the myosin light chain kinase activation

The mathematical model presented here describes the interactions among Ca2+, calmodulin (CaM), and myosin light chain kinase (MLCK) and consists of a kinetic scheme taking into account 7 reactions instead of 12 as proposed previously. We derive a system of 5 nonlinear ordinary differential equations. Solving it yields the prediction of active MLCK as a function of [Ca2+] whereby the active MLCK is defined to be proportional to the Ca4CaM.MLCK complex concentration. The model predictions are compared with other theoretical and experimental predictions of active MLCK as well as with the results of our previously proposed complex model.     

Carbon-fluorine bond activation coupled with carbon-hydrogen bond formation alpha to iridium: kinetics, mechanism, and diastereoselectivity

Reactions of iridium(fluoroalkyl)hydride complexes CpIr(PMe(3))(CF(2)R(F))Y (R(F) = F, CF(3); Y = H, D) with LutHX (Lut = 2,6-dimethylpyridine; X = Cl, I) results in C-F activation coupled with hydride migration to give CpIr(PMe(3))(CYFR(F))X as variable mixtures of diastereomers. Solution conformations and relative diastereomer configurations of the products have been determined by (19)F{(1)H}HOESY NMR to be (S(C), S(Ir))(R(C), R(Ir)) for the kinetic diastereomer and (R(C), S(Ir))(S(C), R(Ir)) for its thermodynamic counterpart. Isotope labeling experiments using LutDCl/CpIr(PMe(3))(CF(2)R(F))H and CpIr(PMe(3))(CF(2)R(F))D/LutHCl) showed that, unlike a previously studied system, H/D exchange is faster than protonation of the alpha-CF bond, giving an identical mixture of product isotopologues from both reaction mixtures. The kinetic rate law shows a first-order dependence on the concentration of iridium substrate, but a half-order dependence on that of LutHCl; this is interpreted to mean that LutHCl dissociates to give HCl as the active protic source for C-F bond activation. Detailed kinetic studies are reported, which demonstrate that lack of complete diastereoselectivity is not a function of the C-F bond activation/H migration steps but that a cationic intermediate plays a double role in loss of diastereoselectivity; the intermediate can undergo epimerization at iridium before being trapped by halide and can also catalyze the epimerization of kinetic diastereomer product to thermodynamic product. A detailed mechanism is proposed and simulations performed to fit the kinetic data.     

Selective control of amino acid metabolism by the GCN2 eIF2 kinase pathway in <Emphasis Type="Italic">Saccharomyces cerevisiae</Emphasis>

Background  

When eukaryotic cells are deprived of amino acids, uncharged tRNAs accumulate and activate the conserved GCN2 protein kinase. Activated Gcn2p up-regulates the general amino acid control pathway through phosphorylation of the translational initiation factor eIF2. In Saccharomyces cerevisiae, Gcn2p is the only kinase that phosphorylates eIF2 to regulate translation through this mechanism. We addressed changes in yeast growth and tRNA aminoacylation, or charging, during amino acid depletion in the presence and absence of GCN2. tRNA charging was measured using a microarray technique which simultaneously measures all cytosolic tRNAs. A fully prototrophic strain, and its isogenic gcn2Δ counterpart, were used to study depletion for each of the 20 amino acids, with a focus on Trp, Arg, His and Leu, which are metabolically distinct and together provide a good overview on amino acid metabolism.     

Insights into the conformational switching mechanism of the human vascular endothelial growth factor receptor type 2 kinase domain

Human vascular endothelial growth factor receptor type 2 (h-VEFGR2) is a receptor tyrosine kinase involved in the angiogenesis process and regarded as an interesting target for the design of anticancer drugs. Its activation/inactivation mechanism is related to conformational changes in its cytoplasmatic kinase domain, involving first among all the αC-helix in N-lobe and the A-loop in C-lobe. Affinity of inhibitors for the active or inactive kinase form could dictate the open or closed conformation of the A-loop, thus making the different conformations of the kinase domain receptor (KDR) domain different drug targets in drug discovery. In this view, a detailed knowledge of the conformational landscape of KDR domain is of central relevance to rationalize the efficiency and selectivity of kinase inhibitors. Here, molecular dynamics simulations were used to gain insight into the conformational switching activity of the KDR domain and to identify intermediate conformations between the two limiting active and inactive conformations. Specific energy barriers have been selectively removed to induce, and hence highlight at the atomistic level, the regulation mechanism of the A-loop opening. The proposed strategy allowed to repeatedly observe the escape of the KDR domain from the DFG-out free energy basin and to identify rare intermediate conformations between the DFG-out and the DFG-in structures to be employed in a structure-based drug discovery process.     

应用非天然氨基酸研究腺苷酸激酶的作用机理

非天然氨基酸定点突变成功地应用在腺苷酸激酶上来研究其作用机理。一个苯丙氨酸的类似物和若干脯氨酸的类似物专一性地接入进腺苷酸激酶。对突变物的稳态动力学研究表明: 酪氨酸-95的芳香性在腺苷酸激酶的催化作用上不起非常重要的作用; 腺苷酸激酶能容耐脯氨酸-17的环变化为大的柔韧的环, 但却不能容耐小的刚硬的四元环。     

The CK2 alpha/CK2 beta interface of human protein kinase CK2 harbors a binding pocket for small molecules

The Ser/Thr kinase CK2 (previously called casein kinase 2) is composed of two catalytic chains (CK2 alpha) attached to a dimer of noncatalytic subunits (CK2 beta). CK2 is involved in suppression of apoptosis, cell survival, and tumorigenesis. To investigate these activities and possibly affect them, selective CK2 inhibitors are required. An often-used CK2 inhibitor is 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole (DRB). In a complex structure with human CK2 alpha, DRB binds to the canonical ATP cleft, but additionally it occupies an allosteric site that can be alternatively filled by glycerol. Inhibition kinetic studies corroborate the dual binding mode of the inhibitor. Structural comparisons reveal a surprising conformational plasticity of human CK2 alpha around both DRB binding sites. After local rearrangement, the allosteric site serves as a CK2 beta interface. This opens the potential to construct molecules interfering with the CK2 alpha/CK2 beta interaction.     

Theoretical study of the Cp2Zr-catalyzed hydrosilylation of ethylene. Reaction mechanism including new sigma-bond activation

The Cp(2)Zr-catalyzed hydrosilylation of ethylene was theoretically investigated with DFT and MP2-MP4(SDQ) methods, to clarify the reaction mechanism and the characteristic features of this reaction. Although ethylene insertion into the Zr-SiH(3) bond of Cp(2)Zr(H)(SiH(3)) needs a very large activation barrier of 41.0 (42.3) kcal/mol, ethylene is easily inserted into the Zr-H bond with a very small activation barrier of 2.1 (2.8) kcal/mol, where the activation barrier and the energy of reaction calculated with the DFT(B3LYP) method are given and in parentheses are those values which have been corrected for the zero-point energy, hereafter. Not only this ethylene insertion reaction but also the coupling reaction between Cp(2)Zr(C(2)H(4)) and SiH(4) easily takes place to afford Cp(2)Zr(H)(CH(2)CH(2)SiH(3)) and Cp(2)Zr(CH(2)CH(3))(SiH(3)) with activation barriers of 0.3 (0.7) and 5.0 (5.4) kcal/mol, respectively. This coupling reaction involves a new type of Si-H sigma-bond activation which is similar to metathesis. The important interaction in the coupling reaction is the bonding overlap between the d(pi)-pi bonding orbital of Cp(2)Zr(C(2)H(4)) and the Si-H sigma orbital. The final step is neither direct C-H nor Si-C reductive elimination, because both reductive eliminations occur with a very large activation barrier and significantly large endothermicity. This is because the d orbital of Cp(2)Zr is at a high energy. On the other hand, ethylene-assisted C-H reductive elimination easily occurs with a small activation barrier, 5.0 (7.5) kcal/mol, and considerably large exothermicity, -10.6 (-7.1) kcal/mol. Also, ethylene-assisted Si-C reductive elimination and metatheses of Cp(2)Zr(H)(CH(2)CH(2)SiH(3)) and Cp(2)Zr(CH(2)CH(3))(SiH(3)) with SiH(4) take place with moderate activation barriers, 26.5 (30.7), 18.4 (20.5), and 28.3 (31.5) kcal/mol, respectively. From these results, it is clearly concluded that the most favorable catalytic cycle of the Cp(2)Zr-catalyzed hydrosilylation of ethylene consists of the coupling reaction of Cp(2)Zr(C(2)H(4)) with SiH(4) followed by the ethylene-assisted C-H reductive elimination.     

Kinetic analysis of the mechanism of plasminogen activation by streptokinase

A kinetic study is made of plasminogen activation to plasmin catalyzed by streptokinase. The goal of the present paper is the resolution of the mechanism corresponding to the activation process by a global way, considering the mechanism as a whole and under less restrictive assumptions that those used by other authors. The kinetic equations describing the evolution with time of species involved in the system have been obtained. These equations are valid for both the transient phase and the steady state of the reaction. A kinetic data analysis procedure to evaluate the kinetic parameters, based on the derived kinetic equations has been suggested, for the first time, in the present paper. The validity of the results obtained has been checked by using simulated progress curves of the species involved. Finally, we have demonstrated that the time course equations obtained can be applied directly to different mechanisms of zymogen activation that could be considered to be particular cases of the general studied mechanism.     

The mechanism of Raf activation through dimerization

Raf, a threonine/serine kinase in the Raf/MEK/ERK pathway, regulates cell proliferation. Raf''s full activation requires dimerization. Aberrant activation through dimerization is an important therapeutic target. Despite its clinical importance, fundamental questions, such as how the side-to-side dimerization promotes the OFF-to-ON transition of Raf''s kinase domain and how the fully activated ON-state kinase domain is stabilized in the dimer for Raf signaling, remain unanswered. Herein, we decipher an atomic-level mechanism of Raf activation through dimerization, clarifying this enigma. The mechanism reveals that the replacement of intramolecular π–π stacking by intermolecular π–π stacking at the dimer interface releases the structural constraint of the αC-helix, promoting the OFF-to-ON transition. During the transition, the inhibitory hydrophobic interactions were disrupted, making the phosphorylation sites in A-loop approach the HRD motif for cis-autophosphorylation. Once fully activated, the ON-state kinase domain can be stabilized by a newly identified functional N-terminal basic (NtB) motif in the dimer for Raf signaling. This work provides atomic level insight into critical steps in Raf activation and outlines a new venue for drug discovery against Raf dimerization.

We decipher an atomic-level mechanism of Raf activation through dimerization, revealing that the disruption of intramolecular π–π stacking at the dimer interface promotes the OFF-to-ON transition.     

Probing the mechanism of sulfoxide-catalyzed hemiacetal activation in dehydrative glycosylation

The concept of sulfoxide-covalent catalysis has been established in the context of a versatile hemiacetal hydroxyl activation/substitution reaction for the formation of anomeric linkages. Mechanistic studies focused on the hemiacetal activation process show that this transformation proceeds in the presence of a sulfonic anhydride and an acid scavenger through the intermediacy of a glycosyl sulfonate species (10), which serves as a resting state prior to the addition of an external nucleophile and subsequent glycosidic bond formation. Successful determination of the proportion of (18)O incorporation in 10 as a function of its formation, via the technique of dynamic monitoring of (13)C-(16/18)O isotopic chemical shift perturbations, provides strong evidence that hemiacetal activation proceeds through initial nucleophilic addition of the hemiacetal hydroxyl to the S(IV)-center of putative sulfonium sulfonate 6. Further confirmation was obtained through the independent synthesis, structure verification, and (1)H NMR detection of glycosyl oxosulfonium 11 during the sulfoxide-catalyzed conversion of hemiacetal 3 to glycosyl sulfonate 10.     

Electrophilic C-H activation at Cp*Ir: ancillary-ligand control of the mechanism of C-H activation

Density functional calculations on the low-temperature cyclometalation of dimethylbenzylamine with [IrCl2Cp*]2/NaOAc have characterized a novel electrophilic activation pathway for C-H bond activation. C-H activation occurs from [Ir(DMBA-H)(kappa2-OAc)Cp*]+, and OAc plays a central role in determining the barrier for reaction. Dissociation of the proximal OAc arm sets up a facile intramolecular deprotonation via a geometrically convenient six-membered transition state. Dissociation of the distal OAc arm, however, leads to a higher energy four-membered (sigma-bond metathesis) transition state, while oxidative addition is even higher in energy. For this Ir3+ system, these three mechanisms appear to lie within a continuum in which the participation of the metal center and an H-accepting ancillary ligand are inversely related. The ability of the ancillary ligand to act as a proton acceptor is the key factor in determining which mechanism pertains.     

Dinuclear chiral vanadium catalysts for oxidative coupling of 2-naphthols via a dual activation mechanism

This review describes our recent efforts in the development of chiral dinuclear vanadium complexes that work as dual activation catalysts for the oxidative coupling of 2-naphthols. The dinuclear vanadium(iv) complex (R(a),S,S)- was prepared by complexation of VOSO(4) with the Schiff base derived from (R)-3,3'-diformyl-2,2'-dihydroxy-1,1'-binaphthyl () and (S)-tert-leucine. Since the dinuclear vanadium(iv) complex was found to be readily oxidized to afford a corresponding vanadium(v) species during preparation in air, a new synthetic procedure using VOCl(3) has been applied towards dinuclear vanadium(v) complexes (R(a),S,S)- and (R(a),S,S)-. To the best of our knowledge, (R(a),S,S)-, and show considerably higher catalytic activity than previously reported vanadium complexes for the oxidative coupling of 2-naphthols.     

Stereoselective alkylation of alpha,beta-unsaturated imines via C-H bond activation

The stereoselective alkylation of alpha,beta-unsaturated imines via C-H activation followed by imine hydrolysis produces tri- and tetrasubstituted alpha,beta-unsaturated aldehydes. In the presence of a rhodium catalyst, alpha,beta-unsaturated N-benzyl imines derived from methacrolein, crotonaldehyde, and tiglic aldehyde undergo directed C-H activation at the beta-position and react with terminal alkenes and alkynes to form the tri- and tetrasubstituted alpha,beta-unsaturated imines with very high stereoselectivity. Hydrolysis to provide alpha,beta-unsaturated aldehydes can be performed under carefully controlled conditions that maintain the stereochemistry of the beta-alkylated imine products. Alternatively, for beta-alkylation products of the N-benzyl imine of methacrolein, hydrolysis can be performed under conditions that provide complete isomerization to the E isomer.     

Fe原子活化乙烷的微观反应机理

本文采用密度泛函理论B3LYP方法在6-311 G(d,p)基组水平上研究了Fe原子催化乙烷反应的微观反应机理,优化了反应过程中各反应物、中间体、过渡态和产物的构型,并在同一水平上计算了反应中各驻点的振动频率,运用自然键轨道理论(NBO)方法分析了各物质的成键情况和轨道间相互作用。Fe原子对乙烷的活化过程可分为C-C键活化及C-H键活化,分别释放出CH4和H2。