Characterization of the transition state of functional enzyme dynamics

Through characterization of the solvent isotope effect on protein dynamics, we have examined determinants of the rate limitation to enzyme catalysis. A global conformational change in Ribonuclease A limits the overall rate of catalytic turnover. Here we show that this motion is sensitive to solvent deuterium content; the isotope effect is 2.2, a value equivalent to the isotope effect on the catalytic rate constant. We further demonstrate that the protein motion possesses a linear proton inventory plot, indicating that a single proton is transferred in the transition state. These results provide compelling evidence for close coupling between enzyme dynamics and function and demonstrate that characterization of the transition state for protein motion in atomic detail is experimentally accessible.     

Pulse dynamics in an excitable reaction – diffusion system

We formulate a theory for pulse dynamics in an excitable reaction‐diffusion system not only in one dimension but also in higher dimensions. In the singular limit where the width of pulse boundaries is infinitesimally thin we derive the equation of motion for a pair of interacting pulses. This equation contains the bifurcation that a motionless pulse loses stability and begins to propagate. The theory predicts the following remarkable properties. When the system is far away from the bifurcation threshold, two propagating pulses merge each other upon head‐on collision. However when the system is close to the threshold the pulses behave as if they are elastic objects. These results are consistent with recent computer simulations.     

Molecular dynamics of the hydrogeniodine reaction system

The molecular dynamics of the hydrogeniodine exchange reaction, H₂ + I₂ ? 2 HI, have been examined in a classical trajectory analysis with trajectories selected within the transition region. The results yield the overall mechanism, the rate and the energy distributions of reactants and products for reaction at 700°K.     

Characterization and dynamics of substituted ruthenacyclobutanes relevant to the olefin cross-metathesis reaction

The reaction of the phosphonium alkylidene [(H(2)IMes)RuCl(2)=CHP(Cy)(3))](+) BF(4)(-) with propene, 1-butene, and 1-hexene at -45 °C affords various substituted, metathesis-active ruthenacycles. These metallacycles were found to equilibrate over extended reaction times in response to decreases in ethylene concentrations, which favored increased populations of α-monosubstituted and α,α'-disubstituted (both cis and trans) ruthenacycles. On an NMR time scale, rapid chemical exchange was found to preferentially occur between the β-hydrogens of the cis and trans stereoisomers prior to olefin exchange. Exchange on an NMR time scale was also observed between the α- and β-methylene groups of the monosubstituted ruthenacycle (H(2)IMes)Cl(2)Ru(CHRCH(2)CH(2)) (R = CH(3), CH(2)CH(3), (CH(2))(3)CH(3)). EXSY NMR experiments at -87 °C were used to determine the activation energies for both of these exchange processes. In addition, new methods have been developed for the direct preparation of metathesis-active ruthenacyclobutanes via the protonolysis of dichloro(1,3-bis(2,4,6-trimethylphenyl)-2-imidazolidinylidene)(benzylidene) bis(pyridine)ruthenium(II) and its 3-bromopyridine analogue. Using either trifluoroacetic acid or silica-bound toluenesulfonic acid as the proton source, the ethylene-derived ruthenacyclobutane (H(2)IMes)Cl(2)Ru(CH(2)CH(2)CH(2)) was observed in up to 98% yield via NMR at -40 °C. On the basis of these studies, mechanisms accounting for the positional and stereochemical exchange within ruthenacyclobutanes are proposed, as well as the implications of these dynamics toward olefin metathesis catalyst and reaction design are described.     

Characterization of the solvation dynamics of an ionic liquid via molecular dynamics simulation

The solvation dynamics of ionic liquids have been the subject of intense experimental study but remain poorly understood. We present the results of molecular dynamics simulations of the solvation dynamics of the ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate in response to photoexcitation of the fluorescent dye coumarin-153. We reproduce the time-resolved fluorescence Stokes shift using linear response theory, then use novel statistical techniques to analyze cation and anion contributions to the signal. We find that the solvation dynamics are dominated by collective ionic motion and characterize the time scale for various features of the collective response. Further, we use the Steele analysis [Mol. Phys. 61, 1031 (1987)] to characterize the contributions to the observed Stokes shift made by translational and rovibrational degrees of freedom. Our results indicate that in contrast to molecular liquids, the rovibrational response is trivial and the observed fluorescence response arises almost entirely from ionic translation. Our results resolve previously open questions in the literature about the nature of the rapid dynamics in room-temperature ionic liquids and offer insight into the physical principles governing ionic liquid behavior on longer time scales.     

PuCO体系的分子反应动力学研究

基于多体项展式理论方法导出的PuCO分子基态(X^7A")的分析势能函数,用准经典的Monte-Carlo轨线法对Pu(^7Fg)+CO(0,0)和O(^3Pg)+PuC(0,0)的分子反应动力学过程进行了计算。结果表明：Pu(^7Fg)与CO(0,0)碰撞易生成PuCO配合物分子,该反应是无阈能反应,反应截面σ随能量Et的升高而下降,当Et=502.1kJ.mol^-^1时,σ几乎为零。O(^3Pg)与PuC(0,0)碰撞易发生生成Pu+CO的交换反应,该反应无阈能。     

Global dynamics of the smallest chemical reaction system with Hopf bifurcation

The global behavior of solutions is described for the smallest chemical reaction system that exhibits a Hopf bifurcation, discovered in [12]. This three-dimensional system is a competitive system and a monotone cyclic feedback system. The Poincaré–Bendixson theory extends to such systems [2,3,6,8] and a Bendixson criterion exists to rule out periodic orbits [4].     

Sequential injection Lab-at-valve (SI-LAV) segmented flow system for kinetic study of an enzyme

A sequential injection-Lab-at-valve (SI-LAV) segmented flow system for kinetic study of an enzyme was developed. Air segments were introduced for separation of enzyme and substrate zones and separation of the stacked zones from the carrier solution which ensure the measurement of the initial rate and minimize the dilution/dispersion effect. The open- ended mixing chamber makes it possible to use air segments in the flow system without the need for additional air segment discarding steps. The enzyme horseradish peroxidase (HRP) kinetic parameters based on initial rate was used as a model study. The operation of the system is virtually the same as that of the conventional batch-wise process. The kinetic parameters (i.e. K(m) and V(max)) of HRP obtained using the proposed system agree well with those obtained using the batch-wise process as well. The proposed system offers additional benefits of volume down scaling, improved rapidity and automatic features that does not require a skillful operator.     

The effect of restricted intramolecular energy flow on the rate of one-substrate enzyme catalyzed reaction

We assume that the free intramolecular energy flow (intramolecular vibrational energy redistribution—IVR) between bonded substrate and enzyme can be restricted due to the presence of a metal atom near the binding site of enzyme. This restriction can represent one of the factors of enzyme catalysis. The concentration of energy evolved during the formation of enzyme-substrate complex in the bonded substrate enhances the reaction rate by several orders of magnitude in comparison with the case of free dissipation of evolved energy into the enzyme.     

Collective reaction behavior of an oscillating system coupled with an excitable reaction

The collective reaction behavior of limit cycles coupled to a nonoscillatory forcing is investigated experimentally and computationally. The coupled chemical system is constructed by adding 1,4-cyclohexanedione (CHD), a species which is capable of forming an oscillator with acidic bromate, into the cerium-catalyzed Belousov-Zhabotinsky reaction. Two levels of coupling exist in the system: (1) through autocatalytic reactions with bromine dioxide radicals and (2) via reactions with oxidized metal catalysts. Experiments illustrate that there is an optimum [1,4-CHD]/[cerium] ratio for inducing complex oscillations, whereas in the 1,4-CHD and malonic acid concentration phase plane two resonant ratios are observed for the onset of complex behavior. In addition, bromate, the oxidant for both suboscillators, also exhibits subtle influences on the complexity of the collective reaction behavior. The experimental observations are qualitatively reproduced with the Field-Koros-Noyes mechanism, modified to account for the coupling reactions with the 1,4-CHD-bromate system.     

Characterization of the switch in the mechanism of an intramolecular Diels-Alder reaction

Changing the dienophile moiety of an intramolecular Diels-Alder (IMDA) cycloaddition from an allyl ether to an allenyl ether can dramatically change the regioselectivity. We hereby show by density functional theory computations that such unprecedented divergence is produced by an underlying change in the mechanism of the reaction. The allyl ether yields a fused tetrahydrofuran through a classical Diels-Alder reaction, whereas the allenyl ether yields a (methylidene)tetrahydropyran through a stepwise process. The latter reaction involves an extreme asynchronism in the bond-forming events with a diradicaloid intermediate that is stabilized by conjugation and synergistic (captodative) effects. Comparison with intermolecular model D-A reactions, which are concerted processes with various degrees of asynchrony, helps explain the change in regioselectivity for the IMDA reaction of allyl systems and the shift in mechanism for the IMDA reaction of the allenyl derivatives studied.     

Gas flow dynamics of an inductively coupled plasma discharge

Temperature and velocity distributions within a low power (0.5–0.75 kW) inductively coupled plasma discharge operating in argon have ben determined for various operating parameters including aerosol gas now rate, plasma gas flow rate, aerosol nozzle diameter, and input power level. All measurements were made without samples. The channel formed in the discharge by the aerosol gas now exhibits temperature and velocity characteristics which distinguishes it from the plasma core and wall regions. Maximum plasma temperature of 8700 ± 300 K and channel gas velocity of 120 $\text{m}\text{s}$ were found.     

Exploiting kinetic spectrophotometric determination of captopril, an angiotensin-converting enzyme inhibitor, in a multi-pumping flow system

The implementation of a differential kinetic spectrophotometric method for the determination of angiotensin-converting-enzyme inhibitors in pharmaceutical formulations is described. The determination method was based on the monitoring (350 nm) of the reaction between captopril and iodate, in the presence of iodide, versus time and was fully automated by exploiting the multi-pumping flow concept. The developed multi-pumping flow system included four discretely actuated solenoid micro-pumps as unique flow manifold active components. The automatic control of the solenoid micro-pumps, under time-based and pulse-counting routines, allowed the implementation of a reliable and versatile analytical determination, with the additional advantage of permitting a runtime access to important analytical parameters, such as flow rate, sample insertion and reagent addition synchronisation, facilitating this way the establishment of an approach for kinetic measurements, directly due to the efficient solution handling and accurate timing control.

A linear range of determination was verified for captopril concentrations between 10.0 and 60.0 μg mL⁻¹ with a sample throughput of about 100 determinations per hour. The results were in agreement with those obtained by the reference procedure with relative deviations between 1.81 and 4.48%.     

Non-RRKM dynamics in the CH3O2 + NO reaction system

Quasi-classical trajectory (QCT) calculations on a model potential energy surface (PES) show strong deviations from statistical Rice-Ramsperger-Kassel-Marcus (RRKM) rate theory for the decomposition reaction (1) CH3OONO* --> CH3O + NO2, where the highly excited CH3OONO* was formed by (2) CH3O2 + NO --> CH3OONO*. The model PES accurately describes the vibrational frequencies, structures, and thermochemistry of the cis- and trans-CH3OONO isomers; it includes cis-trans isomerization in addition to reactions 1 and 2 but does not include nitrate formation, which is too slow to affect the decay rate of CH3OONO*. The QCT results give a strongly time-dependent rate constant for decomposition and damped oscillations in the decomposition rate, not predicted by statistical rate theory. Anharmonicity is shown to play an important role in reducing the rate constant by a factor of 10 smaller than predicted using classical harmonic RRKM theory (microcanonical variational transition state theory). Master equation simulations of organic nitrate yields published previously by two groups assumed that RRKM theory is accurate for reactions 1 and 2 but required surprising parametrizations to fit experimental nitrate yield data. In the present work, it is hypothesized that the non-RRKM rate of reaction (1) and vibrational anharmonicity are at least partly responsible for the surprising parameters.     

Diffusion and reaction in an immobilized enzyme starch saccharification catalyst

Effectiveness factors were predicted from measurements of basic parameters made on single oligosaccharides, and the prediction was compared to experimental effec tiveness factors for the reaction of each oligosaccharide in the immobilized enzyme catalyst. Kinetic parameters were obtained for the hydrolysis of each oligosaccharide catalyzed by soluble glucoamylase, and were fit with a subsite model equation capable of generalization to all sizes of oligosaccharide. Diffusion coefficients in free solution were determined from movement out of a capillary tube. Spatial characteristics of the immobilized enzyme bed were obtained from pulse response experiments, allowing the calculation of effective diffusivities. Experimental effectiveness factors plotted against modulus were in reasonable agreement with the predictions.     

Characterization of a microscale cyclical electrical field flow fractionation system

A microscale cyclical electrical field flow fractionation (CyElFFF) channel is characterized with regard to the effect of various operating parameters and comparison made to recent theoretical developments. Challenges associated with various operating conditions are reported along with some of the optimized operating parameters. The effect of retention wall choice, an offset voltage, relaxation steps, and flow rates, along with the basic operating parameters of voltage, frequency, and electrophoretic mobility are reported. Retention of polystyrene nanoparticle standards is accomplished and the first separations using this technique in a microscale system are also demonstrated. Relaxation steps and offset voltages are found to be effective in eliminating early peaks and in improving plate heights. Plate heights were also found to decrease with increasing flow rates, which is the opposite of the behavior seen in most existing chromatographic systems. The experimental results are compared to the analytical and empirical models of CyElFFF and found to be compatible. Suggestions are made for improving the separation and analysis methods used with CyElFFF.     

Spatiotemporal dynamics of the Landolt reaction in an open spatial reactor with conical geometry

In a previous study, the iodate-sulfite proton autoactivated reaction (Landolt reaction) was shown to exhibit spatial bistability and spatiotemporal oscillations when operated in an open spatial reactor with fixed "thickness", i.e., feed boundary to core distance. Here, we show that the spatial reactors with conical geometry enable one to rapidly probe the sensitivity of the above phenomena over a large range of the "thickness" parameter. This often-neglected parameter in chemical pattern studies plays an important role on the selection and stability of states. We reveal that the quenching capacity of slow diffusing polyacrylate ions on the spatiotemporal oscillations depends on this "thickness". The presented results should be useful for further research on reaction diffusion patterns and chemomechanical structures.