Kinetic Evidence Research Articles

Kinetic evidence: the rate-determining step for ammonia synthesis over electride-supported Ru catalysts is no longer the nitrogen dissociation step

The rate-determining step for ammonia synthesis over Ru catalysts supported by electrides, such as [Ca24Al28O64]4+(e−)4 and Ca2N:e−, is suggested to be the surface reactions of N and H adatoms, in which case the Langmuir–Hinshelwood model should be used to describe the kinetics.

Kinetic evidence for the formation of diazo ethers in the course of reactions between arenediazonium ions and antioxidants

Non-zero, pH-dependent, saturation kinetics are observed in the course of the reaction between 3-methylbenzenediazonium ions and hydroxytyrosol.

Two-Phase Bactericidal Mechanism of Silver Nanoparticles against Burkholderia pseudomallei.

Silver nanoparticles (AgNPs) have a strong antimicrobial activity against a variety of pathogenic bacteria. The killing mechanism of AgNPs involves direct physical membrane destruction and subsequent molecular damage from both AgNPs and released Ag+. Burkholderia pseudomallei is the causative agent of melioidosis, an endemic infectious disease primarily found in northern Australia and Southeast Asia. B. pseudomallei is intrinsically resistant to most common antibiotics. In this study, the antimicrobial activity and mechanism of AgNPs (10–20 nm) against B. pseudomallei were investigated. The MIC and MBC for nine B. pseudomallei strains ranged from 32–48 μg/mL and 96–128 μg/mL, respectively. Concentrations of AgNPs less than 256 μg/mL were not toxic to human red blood cells. AgNPs exhibited a two-phase mechanism: cell death induction and ROS induction. The first phase was a rapid killing step within 5 min, causing the direct damage of the cytoplasmic membrane of the bacterial cells, as observed by a time-kill assay and fluorescence microscopy. During the period of 5–30 min, the cell surface charge was rapidly neutralized from -8.73 and -7.74 to 2.85 and 2.94 mV in two isolates of B. pseudomallei, as revealed by zeta potential measurement. Energy-dispersive X-ray (EDX) spectroscopy showed the silver element deposited on the bacterial membrane, and TEM micrographs of the AgNP-treated B. pseudomallei cells showed severe membrane damage and cytosolic leakage at 1/5 MIC and cell bursting at MBC. During the killing effect the released Ag+ from AgNPs was only 3.9% from the starting AgNPs concentration as observed with ICP-OES experiment. In the second phase, the ROS induction occurred 1–4 hr after the AgNP treatment. Altogether, we provide direct kinetic evidence of the AgNPs killing mechanism, by which cell death is separable from the ROS induction and AgNPs mainly contributes in the killing action. AgNPs may be considered a potential candidate to develop a novel alternative agent for melioidosis treatment with fast action.

IQGAP1 Interaction with RHO Family Proteins Revisited: KINETIC AND EQUILIBRIUM EVIDENCE FOR MULTIPLE DISTINCT BINDING SITES

IQ motif-containing GTPase activating protein 1 (IQGAP1) plays a central role in the physical assembly of relevant signaling networks that are responsible for various cellular processes, including cell adhesion, polarity, and transmigration. The RHO family proteins CDC42 and RAC1 have been shown to mainly interact with the GAP-related domain (GRD) of IQGAP1. However, the role of its RASGAP C-terminal (RGCT) and C-terminal domains in the interactions with RHO proteins has remained obscure. Here, we demonstrate that IQGAP1 interactions with RHO proteins underlie a multiple-step binding mechanism: (i) a high affinity, GTP-dependent binding of RGCT to the switch regions of CDC42 or RAC1 and (ii) a very low affinity binding of GRD and a C terminus adjacent to the switch regions. These data were confirmed by phosphomimetic mutation of serine 1443 to glutamate within RGCT, which led to a significant reduction of IQGAP1 affinity for CDC42 and RAC1, clearly disclosing the critical role of RGCT for these interactions. Unlike CDC42, an extremely low affinity was determined for the RAC1-GRD interaction, suggesting that the molecular nature of IQGAP1 interaction with CDC42 partially differs from that of RAC1. Our study provides new insights into the interaction characteristics of IQGAP1 with RHO family proteins and highlights the complementary importance of kinetic and equilibrium analyses. We propose that the ability of IQGAP1 to interact with RHO proteins is based on a multiple-step binding process, which is a prerequisite for the dynamic functions of IQGAP1 as a scaffolding protein and a critical mechanism in temporal regulation and integration of IQGAP1-mediated cellular responses.

Evidence of compensatory joint kinetics during stair ascent and descent in Parkinson’s disease

BackgroundStair ambulation is a challenging activity of daily life that requires larger joint moments than walking. Stabilisation of the body and prevention of lower limb collapse during this task depends upon adequately-sized hip, knee and ankle extensor moments. However, people with Parkinson’s disease (PD) often present with strength deficits that may impair their capacity to control the lower limbs and ultimately increase their falls risk. ObjectiveTo investigate hip, knee and ankle joint moments during stair ascent and descent and determine the contribution of these joints to the body’s support in people with PD. MethodsTwelve PD patients and twelve age-matched controls performed stair ascent and descent trials. Data from an instrumented staircase and a three-dimensional motion analysis system were used to derive sagittal hip, knee and ankle moments. Support moment impulses were calculated by summing all extensor moment impulses and the relative contribution of each joint was calculated. ResultsLinear mixed model analyses indicated that PD patients walked slower and had a reduced cadence relative to controls. Although support moment impulses were typically not different between groups during stair ascent or descent, a reduced contribution by the ankle joint required an increased knee joint contribution for the PD patients. ConclusionsDespite having poorer knee extensor strength, people with PD rely more heavily on these muscles during stair walking. This adaptation could possibly be driven by the somewhat restricted mobility of this joint, which may provide these individuals with an increased sense of stability during these tasks.

Periodic protein adsorption at the gold/biotin aqueous solution interface: evidence of kinetics with time delay.

An oscillatory molecular adsorption pattern of the protein neutravidin from aqueous solution onto gold, in presence of a pre-deposited self assembled mono-molecular biotin film, is reported. Real time surface Plasmon resonance sensing was utilized for evaluation of the adsorption kinetics. Two different fractions were identified: in the initial phase, protein molecules attach irreversibly onto the Biotin ligands beneath towards the jamming limit, forming a neutravidin-biotin fraction. Afterwards, the growth rate exhibits distinct, albeit damped adsorption-desorption oscillations over an extended time span, assigned to a quasi reversibly bound fraction. These findings agree with, and firstly confirm a previously published model, proposing macro-molecular adsorption with time delay. The non-linear dynamic model is applicable to and also resembles non-damped oscillatory binding features of the hetero-catalytic oxidation of carbon monoxide molecules on platinum in the gas phase. An associated surface residence time can be linked to the dynamics and time scale required for self-organization.

DNA Polymerase ν Rapidly Bypasses O6-Methyl-dG but Not O6-[4-(3-Pyridyl)-4-oxobutyl-dG and O2-Alkyl-dTs.

4-(Methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) is a potent tobacco carcinogen that forms mutagenic DNA adducts including O6-methyl-2'-deoxyguanosine (O6-Me-dG), O6-[4-(3-pyridyl)-4-oxobut-1-yl]-dG (O6-POB-dG), O2-methylthymidine (O2-Me-dT), and O2-POB-dT. We evaluated the ability of human DNA polymerase ν to bypass this damage to evaluate the structural constraints on substrates for pol ν and to evaluate if there is kinetic evidence suggesting the in vivo activity of pol ν on tobacco-induced DNA damage. Presteady-state kinetic analysis has indicated that O6-Me-dG is a good substrate for pol ν, while O6-POB-dG and the O2-alkyl-dT adducts are poor substrates for pol ν. The reactivity with O6-Me-dG is high with a preference for dCTP > dGTP > dATP > dTTP. The catalytic activity of pol ν toward O6-Me-dG is high and can potentially be involved in its bypass in vivo. In contrast, pol ν is unlikely to bypass O6-POB-dG or the O2-alkyl-dTs in vivo.

Solvent-, Silver-, and Acid-Free NHC-Au-X Catalyzed Hydration of Alkynes. The Pivotal Role of the Counterion

NHC-Au-X (NHC = 1,3-bis(2,6-diisopropylphenyl)imidazol-2-ylidene, X– = BArF–, BF4–, SbF6–, OTf–, NTf2–, ClO4–, OTs–, TFA–) catalysts were tested in the hydration of alkynes. A complete rationalization of the counterion effect enabled us to develop a highly efficient methodology under solvent-, silver-, and acid-free conditions. Thus, it was possible to use room or mild (60 °C) temperature and to reduce the catalyst loading up to 0.01 mol % with respect to the substrate, leading to high TON (104) and TOF (103 h–1) values. The favorable catalytic conditions allowed us to reach very low E factor (0.03–0.06) and high EMY (94–97) values. Finally, the absence of solvent permits easy separation of the liquid product from solid catalyst and ionic additives by distillation, giving products with high purity that are uncontaminated by metals. This opens the way to catalyst recycling (up to four times) without loss of activity. The overall catalytic and kinetic evidence, supported by computational results, confirms t...

Kinetic Study on Multielectron-Transfer Mechanism for Flake-Ball-Shaped Bismuth-Tungstate Photocatalyst

It has been reported that flake ball (FB)-shaped particulate bismuth tungstate (Bi2WO6: BTO) particles prepared by hydrothermal method exhibit photocatalytic activity for oxidative decomposition of organic compounds comparable to that of a commercial titania photocatalyst, while the activity for methanol dehydrogenation is relatively low even with platinum-loaded ones [1]. These facts suggest that two (or four)-electron transfer to the surface-adsorbed oxygen (O2), requiring more anodic potential of electrons in photocatalyst particles, happens in FB-BTO, but no report on the evidence for the multielectron-transfer mechanism have been published. In this study, light-intensity dependence of the rate of acetic-acid decomposition was investigated to obtain kinetic evidence for the multielectron transfer. FB-BTO, composed of particles of spherical assembly of BTO flakes, was prepared following the previous report [1]. As-prepared FB, its ball-milled samples (L and H) and their 773 K-calcined samples (500FB, 500L and 500H) were used for decomposition of acetic acid in aerobic aqueous suspensions under monochromatic photoirradiation by (A) a diffraction grating-type illuminator (Jasco CRM-FD; maximum 10 mW) or (B) a 365-nm UV-LED (maximum 320 mW). Figure 1 shows order (n) of light-intensity dependences at four wavelengths (irradiation A) calculated by assuming; r = a × I n (r: rate, a: constant and I: light intensity). Except for the samples L and H at 380 and 410 nm, BTO showed almost first-order light-intensity dependences at wavelengths between 320 and 410 nm. With the higher intensity irradiation (irradiation B), the order was decreased to ca. 0.5 order for FB and L as shown in Fig. 2. As has been reported previously, photocatalytic acetic-acid decomposition proceeds through radical-chain mechanism with an alkyl peroxy radical as a chain carrier when titania was used as a photocatalyst, and the order of light-intensity dependence was ca. 0.5 [2]. The above-mentioned first-order light-intensity dependence for the most BTO samples can be interpreted by combination of second-order dependence for the accumulation of two electrons to reduce O2 and 0.5-order dependence owing to the radical-chain mechanism. Difference in folding points of plots in Fig. 2 between FB and L was observed; a folding point for FB was appreciably lower than that of L. One of the possible reasons for this difference is that the probability of the second-photon absorption by one photon-absorbed FB particle within its lifetime is higher than that of L particle owing to larger volume of FB particles. [1] F. Amano, K. Nogami, R. Abe, B. Ohtani, J. Phys. Chem. C. 112, 9320 (2008). [2] T. Torimoto, Y. Aburakawa, Y. Kawahara, S. Ikeda, and B. Ohtani, Chem. Phys. Lett., 392, 220 (2004). Figure 1

Exploring the concurrence of phase transition and grain growth in nanostructured alloy

In nanostructured alloys, the concurrence of (solid-state) grain growth and phase transition is ubiquitously observed; however, due to the lack of kinetic evidences, the underlying physics of concurrence remains scarcely understood. In this study, for nanostructured Fe alloy as a model system, macro- and micro-scale characterizations for the concurrence were carried out using in situ X-ray diffraction and in situ high-resolution transmission electron microscopy (HRTEM). Macroscopically, the grain growth occurs and ceases before the end of phase transition, and microscopically, the concurrence of grain boundary (GB) and phase boundary (PB) migrations was certified as well. These experimental results, together with the ex situ HRTEM and molecular dynamics simulation, uncovered the interaction between GB and PB migrations, i.e., both velocity and direction of the PB migration are influenced when the PB interacts with the GB. On this basis, the concurrence was utilized to produce a new kind of heterogeneous and hierarchical microstructure (i.e., dual-phase bimodal nanostructure). The present findings, yield a deep understanding of the phase transition in nanostructured alloys, and further, demonstrate the potential usage of concurrence in manipulating the nanostructures for the development of nanostructured alloys.

Intrinsic relative nucleophilicity of indoles

The range of applicability of intrinsic (i.e., electronic) relative indices for quantifying electrophilicity and nucleophilicity responses (Chamorro et al. in J Phys Chem A 117(12):2636–2643, 2013) is extended to the characterization of coupling reactions of indoles with benzhydrylium ions and with the strongly electron-deficient heteroarene 4,6-dinitrobenzofuroxan. The reactivity categorization based on experimental kinetic evidence for such a electrophile/nucleophile coupling (Lakhdar et al. in J Org Chem 71(24):9088–9095, 2006) is rationalized in terms of purely electronic descriptors, revealing the polar nucleophilic activation of indole as a key factor associated with the initial rate-determining C–C coupling process.

Distributive Processing by the Iron(II)/α-Ketoglutarate-Dependent Catalytic Domains of the TET Enzymes Is Consistent with Epigenetic Roles for Oxidized 5-Methylcytosine Bases

The ten-eleven translocation (TET) proteins catalyze oxidation of 5-methylcytosine ((5m)C) residues in nucleic acids to 5-hydroxymethylcytosine ((5hm)C), 5-formylcytosine ((5f)C), and 5-carboxycytosine ((5ca)C). These nucleotide bases have been implicated as intermediates on the path to active demethylation, but recent reports have suggested that they might have specific regulatory roles in their own right. In this study, we present kinetic evidence showing that the catalytic domains (CDs) of TET2 and TET1 from mouse and their homologue from Naegleria gruberi, the full-length protein NgTET1, are distributive in both chemical and physical senses, as they carry out successive oxidations of a single (5m)C and multiple (5m)C residues along a polymethylated DNA substrate. We present data showing that the enzyme neither retains (5hm)C/(5f)C intermediates of preceding oxidations nor slides along a DNA substrate (without releasing it) to process an adjacent (5m)C residue. These findings contradict a recent report by Crawford et al. ( J. Am. Chem. Soc. 2016 , 138 , 730 ) claiming that oxidation of (5m)C by CD of mouse TET2 is chemically processive (iterative). We further elaborate that this distributive mechanism is maintained for TETs in two evolutionarily distant homologues and posit that this mode of function allows the introduction of (5m)C forms as epigenetic markers along the DNA.

C−H Activation of Methane to Syngas on MnxCe1−x−yZryO2: A Molecular Beam Study

AbstractMn‐doped ceria zirconia thin films (MnxCe1−x−yZryO2, MCZ) were employed as flat model catalyst surfaces for CH4 activation. MCZ films exhibit characteristics of single crystal and powder materials, such as smooth surfaces and porosity. From molecular‐beam studies, it has been identified that the oxygen storage capacity increases with Mn content. Mutually exclusive observation of H2O or a mixture of products (CO2+CO+H2) occurs, when the reactants was allowed to react directly on MCZ, underscoring their formation or prevention (and consumption), respectively. The results suggest that there is competition and cooperation among different elementary reactions under complementary conditions. From a significant partial oxidation of CH4 through C−H activation, it is found that formation of syngas begins at 700 K and the reaction rate increases with increasing temperature. Kinetic evidences indicate that the reaction proceeds through a combustion–reformation pathway.

Kinetic evidence of magnetic reconnection due to Kelvin‐Helmholtz waves

AbstractThe Kelvin‐Helmholtz (KH) instability at the Earth's magnetopause is predominantly excited during northward interplanetary magnetic field (IMF). Magnetic reconnection due to KH waves has been suggested as one of the mechanisms to transfer solar wind plasma into the magnetosphere. We investigate KH waves observed at the magnetopause by the Magnetospheric Multiscale (MMS) mission; in particular, we study the trailing edges of KH waves with Alfvénic ion jets. We observe gradual mixing of magnetospheric and magnetosheath ions at the boundary layer. The magnetospheric electrons with energy up to 80 keV are observed on the magnetosheath side of the jets, which indicates that they escape into the magnetosheath through reconnected magnetic field lines. At the same time, the low‐energy (below 100 eV) magnetosheath electrons enter the magnetosphere and are heated in the field‐aligned direction at the high‐density edge of the jets. Our observations provide unambiguous kinetic evidence for ongoing reconnection due to KH waves.

Mechanistic insights on C[sbnd]O and C[sbnd]C bond activation and hydrogen insertion during acetic acid hydrogenation catalyzed by ruthenium clusters in aqueous medium

Catalytic pathways for acetic acid (CH3COOH) and hydrogen (H2) reactions on dispersed Ru clusters in the aqueous medium and the associated kinetic requirements for CO and CC bond cleavages and hydrogen insertions are established from rate and isotopic assessments. CH3COOH reacts with H2 in steps that either retain its carbon backbone and lead to ethanol, ethyl acetate, and ethane (47–95%, 1–23%, and 2–17% carbon selectivities, respectively) or break its CC bond and form methane (1–43% carbon selectivities) at moderate temperatures (413–523K) and H2 pressures (10–60bar, 298K). Initial CH3COOH activation is the kinetically-relevant step, during which CH3C(O)OH bond cleaves on a metal site pair at Ru cluster surfaces nearly saturated with adsorbed hydroxyl (OH∗) and acetate (CH3COO∗) intermediates, forming an adsorbed acetyl (CH3CO∗) and hydroxyl (OH∗) species. Acetic acid turnover rates increase proportionally with both H2 (10–60bar) and CH3COOH concentrations at low CH3COOH concentrations (<0.83M), but decrease from first to zero order as the CH3COOH concentration and the CH3COO∗ coverages increase and the vacant Ru sites concomitantly decrease. Beyond the initial CH3C(O)OH bond activation, sequential H-insertions on the surface acetyl species (CH3CO∗) lead to C2 products and their derivative (ethanol, ethane, and ethyl acetate) while the competitive CC bond cleavage of CH3CO∗ causes the eventual methane formation. The instantaneous carbon selectivities toward C2 species (ethanol, ethane, and ethyl acetate) increase linearly with the concentration of proton-type Hδ+ (derived from carboxylic acid dissociation) and chemisorbed H∗. The selectivities toward C2 products decrease with increasing temperature, because of higher observed barriers for CC bond cleavage than H-insertion. This study offers an interpretation of mechanism and energetics and provides kinetic evidence of carboxylic acid assisted proton-type hydrogen (Hδ+) shuffling during H-insertion steps in the aqueous phase, unlike those in the vapor phase, during the hydrogenation of acetic acid on Ru clusters.

Two separate though interconnected routes underlie NADH and succinate oxidation: kinetic evidence for different functional compartments of Coenzyme Q and/or Complex III

Two separate though interconnected routes underlie NADH and succinate oxidation: kinetic evidence for different functional compartments of Coenzyme Q and/or Complex III

Kinetic Evidence for Reactive Dimeric TAML Iron Species in the Catalytic Oxidation of NADH and a Dye by O2 in AOT Reverse Micelles

The efficacy of the iron(III) TAML activator [Fe{C6H4-1,2-(N1COCMe2N2CO)2CMe2(Fe–N1)(Fe–N2)}(OH2)]− (1) for the catalytic activation of dioxygen in reverse micelles of Aerosol OT (AOT) in n-octane has been studied. Kinetic evidence is presented for the existence of unusual second-order catalytic pathways in the oxidation of NADH to NAD+ and the bleaching of blue pinacyanol chloride (PNC) dye. Depending on the substrate and reaction conditions, a second-order pathway in [1] either dominates or proceeds in obvious combination with a first-order pathway in [1]. Detailed kinetic analysis of the experimental data supports the previously made hypothesis that the reactive intermediate is associated with the mixed-valent dimer system [LFeIIIOFeIVL]3–/[LFeIII(OH)FeIVL]2–.

Cerium(IV) Oxidations Of Sulfated Polysaccharides In Aqueous Perchlorate Solutions: A Kinetic And Mechanistic Approach

The kinetics of oxidation of iota- and lambda-carrageenans as sulfated polysaccharides by cerium(IV) was studied spectrophotometrically in aqueous perchlorate solutions at a fixed ionic strength of 2.0 mol dm -3 and a temperature of 25 o C. The reactions showed a first order dependence on (Ce IV ), whereas the orders with respect to each carrageenan concentration were less than unity. The reactions exhibited fractional-first order kinetics with respect to (H + ). Increasing ionic strength increased the oxidation rates. The oxidation products of carrageenans were characterized by elemental analysis and IR spectra as their diketo-acid derivatives. The oxidation products were found to have high tendencies to form coordination polymer complexes with some metal cations such as Ba II , Cd II , Pb II and Ag I . Kinetic evidences for the formation of 1:1 complexes were revealed. Plausible mechanistic scheme for cerium(IV) oxidations of carrageenans were proposed. The activation parameters with respect to the slow step of the reactions were evaluated and discussed. The rate laws have been derived and the reaction constants involved in the different steps of the mechanisms were calculated. The activation parameters associated with the rate- determining step of the mechanism along with thermodynamic quantities of the equilibrium constants were computed and discussed. Copyright © 2016 VBRI Press.

Kinetic Aspects of the Interaction between Ligand and G Protein-Coupled Receptor: The Case of the Adenosine Receptors.

Ligand-receptor binding kinetics is an emerging topic in the drug research community. Over the past years, medicinal chemistry approaches from a kinetic perspective have been increasingly applied to G protein-coupled receptors including the adenosine receptors (AR), which are involved in a plethora of physiological and pathological conditions. The study of ligand-AR binding kinetics offers room for detailed structure-kinetics relationships next to more traditional structure-activity relationships. Their combination may facilitate the triage of candidate compounds in hit-to-lead campaigns. Furthermore, kinetic studies also help in understanding AR allosterism. Allosteric modulation may yield a change in the activity and conformation of a receptor resulting from the binding of a compound at a site distinct from where the endogenous agonist adenosine binds. Hence, in this Review, we summarize available data and evidence for the binding kinetics of orthosteric and allosteric AR ligands. We hope this Review will raise awareness to consider the kinetic aspects of drug-target interactions on both ARs and other drug targets.

Extensive Experimental and Computational Study of Counterion Effect in the Reaction Mechanism of NHC-Gold(I)-Catalyzed Alkoxylation of Alkynes

Herein, we synthesized and characterized through NMR and X-ray techniques a new set of [(NHC)-Au-X] complexes (NHC = 1,3-bis(2,6-diisopropylphenyl)-imidazol-2-ylidene), differing in the counterion X– (X– = OMs–, NO3–, ClO4–, 2,2,3,3,4,4,5,5,6,6,7,7,7-tridecafluoroheptanoate (PFHp–)). All of these complexes, together with those already known having NTf2– and phthalimide (ptm–) as counterions, were tested as catalysts in the methoxylation of 3-hexyne. The results were analyzed together with those obtained previously. The values of activation parameters (ΔH⧧ and ΔS⧧) for different anions are also reported. The overall catalytic and kinetic evidence, together with an extensive computational work, confirm the general mechanistic picture given recently in which the anion plays an active role in all steps of the reaction mechanism: pre-equilibrium, nucleophilic attack, and protodeauration. Medium-coordinating anions (OMs–, OTs–) containing a highly symmetric anchoring group give the best catalytic performances. ...