Forward Rate Constants Research Articles

Kinetic modelling of dissolution dynamic nuclear polarisation 13 C magnetic resonance spectroscopy data for analysis of pyruvate delivery and fate in tumours.

Dissolution dynamic nuclear polarisation (dDNP) of 13 C-labelled pyruvate in magnetic resonance spectroscopy/imaging (MRS/MRSI) has the potential for monitoring tumour progression and treatment response. Pyruvate delivery, its metabolism to lactate and efflux were investigated in rat P22 sarcomas following simultaneous intravenous administration of hyperpolarised 13 C-labelled pyruvate (13 C1 -pyruvate) and urea (13 C-urea), a nonmetabolised marker. A general mathematical model of pyruvate-lactate exchange, incorporating an arterial input function (AIF), enabled the losses of pyruvate and lactate from tumour to be estimated, in addition to the clearance rate of pyruvate signal from blood into tumour, Kip , and the forward and reverse fractional rate constants for pyruvate-lactate signal exchange, kpl and klp . An analogous model was developed for urea, enabling estimation of urea tumour losses and the blood clearance parameter, Kiu . A spectral fitting procedure to blood time-course data proved superior to assuming a gamma-variate form for the AIFs. Mean arterial blood pressure marginally correlated with clearance rates. Kiu equalled Kip , indicating equivalent permeability of the tumour vasculature to urea and pyruvate. Fractional loss rate constants due to effluxes of pyruvate, lactate and urea from tumour tissue into blood (kpo , klo and kuo , respectively) indicated that T1 s and the average flip angle, θ, obtained from arterial blood were poor surrogates for these parameters in tumour tissue. A precursor-product model, using the tumour pyruvate signal time-course as the input for the corresponding lactate signal time-course, was modified to account for the observed delay between them. The corresponding fractional rate constant, kavail , most likely reflected heterogeneous tumour microcirculation. Loss parameters, estimated from this model with different TRs, provided a lower limit on the estimates of tumour T1 for lactate and urea. The results do not support use of hyperpolarised urea for providing information on the tumour microcirculation over and above what can be obtained from pyruvate alone. The results also highlight the need for rigorous processes controlling signal quantitation, if absolute estimations of biological parameters are required.

A computer-aided method for controlling chemical resistance of drugs using RRKM theory in the liquid phase

The chemical resistance of drugs against any change in their composition and studying the rate of multiwell-multichannel reactions in the liquid phase, respectively, are the important challenges of pharmacology and chemistry. In this article, we investigate two challenges together through studying drug stability against its unimolecular reactions in the liquid phase. Accordingly, multiwell-multichannel reactions based on 1,4-H shifts are designed for simplified drugs such as 3-hydroxyl-1H-pyrrol-2(5H)-one, 3-hydroxyfuran-2(5H)-one, and 3-hydroxythiophen-2(5H)-one. After that, the reverse and forward rate constants are calculated by using the Rice Ramsperger Kassel Marcus theory (RRKM) and Eckart tunneling correction over the 298–360 K temperature range. Eventually, using the obtained rate constants, we can judge drug resistance versus structural changes. To attain the goals, the potential energy surfaces of all reactions are computed by the complete basis set-quadratic Becke3 composite method, CBS-QB3, and the high-performance meta hybrid density functional method, M06-2X, along with the universal Solvation Model based on solute electron Density, SMD, due to providing more precise and efficient results for the barrier heights and thermodynamic studies. To find the main reaction pathway of the intramolecular 1,4-H shifts in the target molecules, all possible reaction pathways are considered mechanistically in the liquid phase. Also, the direct dynamics calculations that carry out by RRKM theory on the modeled pathways are used to distinguish the main reaction pathway. As the main finding of this research, the results of quantum chemical calculations accompanied by the RRKM/Eckart rate constants are used to predict the stability of drugs. This study proposes a new way to examine drug stability by the computer-aided reaction design of target drugs. Our results show that 3-hydroxyfuran-2(5H)-one based drugs are the most stable and 3-hydroxythiophen-2(5H)-one based drugs are more stable than 3-hydroxy-1H-pyrrol-2 (5H)-one based drugs in water solution.

Rational Design and Synthesis of OEP and TPP Centered Phosphorus(V) Porphyrin-Naphthalene Conjugates: Triplet Formation via Rapid Charge Recombination.

Six new "axial-bonding" type "phosphorus(V) porphyrin-naphthalene" conjugates have been prepared consisting of octaethylporphyrinatophosphorus(V) (POEP+)/tetraphenylporphyrinatophosphorus(V) (PTPP+) and naphthalene (NP). The distance between the porphyrin and NP was systematically varied using polyether bridges. The unique structural topology of the octaethylporphyrinatophosphorus(V) (POEP+) and tetraphenylporphyrinatophosphorus(V) (PTPP+) enabled construction of mono- and disubstituted phosphorus(V) porphyrin-naphthalene conjugates, respectively. The steady-state and transient spectral properties were investigated as a function of redox properties, distance, and molecular topology. Strong electronic interactions between the phosphorus(V) porphyrin and NP in directly bound conjugates were observed. The established energy diagrams predicted reductive electron transfer involving singlet excited phosphorus(V) porphyrin and NP to generate high-energy (∼1.83-2.11 eV) charge-separated states (POEP/PTPP)•-(NP)•+. Femtosecond transient absorption spectral studies revealed rapid deactivation of singlet excited phosphorus(V) porphyrin due to charge separation wherein the estimated forward rate constants were in the range of 109-1010 s-1 and were dependent on the distance between the NP and porphyrins units, as well as the redox potentials of the type of the phosphorus(V) porphyrin. Additionally, due to high exothermicity and low-lying triplet states, the charge recombination process was found to be rapid, leading to populating the triplet states of phosphorus(V) porphyrins.

Global Master Equation Analysis of Rate Data for the Reaction C2H4 + H ⇄ C2H5: ΔfH0⊖C2H5.

While forward and reverse rate constants are frequently used to determine enthalpies of reaction and formation, this process is more difficult for pressure-dependent association/dissociation reactions, especially since the forward and reverse reactions are usually studied at very different temperatures. The problems can be overcome by using a data-fitting procedure based on a master equation model. This approach has been applied to existing experimental pressure-dependent forward and reverse rate coefficients for the reaction C2H4 + H ⇄ C2H5 (k1, k-1) using the MESMER code to determine ΔfH0⊖C2H5 from the enthalpy of the reaction. New measurements of k1, k-1 were included in analysis. They are based on laser flash photolysis with direct observation of H atom time profiles by vacuum ultraviolet laser-induced fluorescence under conditions where the approach to equilibrium could be observed. Measurements were made over the temperature range 798-828 K and with [He] from 2.33 to 7.21 × 1018 molecule cm-3. These data were then combined with a wide range of existing experimental data with helium as the bath gas (112 measurements of k1 and k-1, covering the temperature range 285-1094 K, and [He] = 7.1 × 1015-1.9 × 1019 molecule cm-3) and fitted using the master equation solver MESMER. The required vibrational frequencies and rotational constants of the system were obtained from ab initio calculations, and the activation threshold for association (ΔEthresh), enthalpy of reaction (ΔrH0⊖), imaginary frequency (υimag), and helium energy-transfer parameters (⟨ΔE⟩d,298(T/298)n) were optimized. The resulting parameters (errors are 2σ) are ΔEthresh = 11.43 ± 0.34 kJ mol-1, ΔrH0⊖ = -145.34 ± 0.60 kJ mol-1, υimag = 730 ± 130 cm-1, ⟨ΔE⟩d,298 = 54.2 ± 7.6 cm-1, and n = 1.17 ± 0.12. A value of ΔfH298.15⊖(C2H5) = 120.49 ± 0.57 kJ mol-1 is obtained by combining ΔrH0⊖ with standard enthalpies of formation for H and C2H4 and making the appropriate temperature corrections. The dependence of these parameters on how the internal rotor and CH2 inversion modes are treated has been explored. The experimental data for other bath gases have been analyzed, and data sets compatible with the potential energy surface parameters determined above have been identified. The parameters are virtually identical but with slightly smaller error limits. Parameterization of k1, k-1 using the Troe formalization has been used to investigate competition between ethyl decomposition and reaction with oxygen under combustion conditions.

Leveraging De Donder relations for a thermodynamically rigorous analysis of reaction kinetics in liquid media

This Mini-review considers the use of De Donder relations to facilitate a thermodynamically rigorous discussion of liquid-phase reaction kinetics through the analysis of elementary steps. In quantifying “solvent effects,” pure species reference states are convenient. Rate expressions developed with this convention capture all effects of thermodynamic non-ideality in solvent-specific activity coefficients or excess free energies, whereas commonly applied infinite dilution reference states lead to solvent- and composition-dependent standard-state rate and equilibrium constants. Two solvent effects are described: a “kinetic” effect, which comprises solvation of a transition state relative to reactants in an elementary step, and a “thermodynamic” effect, which comprises solvation of products relative to reactants in an elementary step. The former impacts the forward rate constant, and the latter impacts the reversibility. These effects are formally encoded in De Donder rate expressions; thus, they inherently account for solvation while maintaining thermodynamic consistency with respect to elementary rate and equilibrium constants. A series of case studies are presented. These demonstrate that solvent effects can lead to substantial deviations from anticipated behavior during routine analysis of liquid-phase reactions. Additionally, we find that surface reactions and degree of rate control in multi-reaction sequences can be impacted by bulk solvation, but such effects are difficult to predict a priori.

Beyond the Laviron Method: A New Mathematical Treatment for Analyzing the Faradaic Current in Reversible, Quasi-Reversible, and Irreversible Cyclic Voltammetry of Adsorbed Redox Species.

A new algorithm that describes the faradaic current for elementary redox reactions in the cyclic voltammetric responses of persistently adsorbed species on metal electrodes at any scan rate is presented. This work does not assume electrochemical reversibility and instead demonstrates a set of equations that encapsulate how the forward and back charge-transfer rate constants influence the data as a function of the experimental time scale. The method presented here is compared against other approaches that rely on either finite-difference calculations or that require numerical approximation of improper integrals (i.e., ±infinity as a bound). The method here demonstrates that the current-potential data can be described by incomplete gamma functions, whose two arguments capture the relevant kinetic variables. Following the notation for the Butler-Volmer model of charge transfer, exact solutions are presented for the cases of the charge-transfer coefficient, α, equal to 1 or 0. A related algorithm based on these results affords calculation of current-potential data for 0 < α < 1, allowing comprehensive analysis (i.e., point by point) of voltammetric data throughout the reversible, quasi-reversible, and irreversible regimes. Accordingly, this work represents an alternative to the method of Laviron, i.e., analyzing just the peak splitting values, for experimentalists to understand and interpret their voltammetric data in totality.

Diffusive barrier crossing rates from variationally determined eigenvalues.

Kramers' procedure for calculating the rate of activated processes involves partitioning space into reactant, barrier, and product regions by introducing two dividing surfaces. Then, a nonequilibrium steady state is established by injecting particles on one surface and removing them when they reach the other. The rate is obtained as the ratio of the steady-state flux between the surfaces and the population of the initial well. An alternative procedure that seems less artificial is to estimate the first non-zero eigenvalue of the operator that describes the dynamics and then equate its magnitude to the sum of the forward and backward rate constants. Here, we establish the relationship between these approaches for diffusive dynamics, starting with the variational principle for the eigenvalue of interest and then using a trial function involving two adjustable surfaces. We show how Kramers' flux-over-population expression for the rate constant can be obtained from our variationally determined eigenvalue in the special case where the reactant and product regions are separated by a high barrier. This work exploits the modern theory of activated rate processes where the committor (the probability of reaching one dividing surface before the other) plays a central role. Surprisingly, our upper bound for the eigenvalue can be expressed solely in terms of mean first-passage times and the mean transition-path time between the two dividing surfaces.

EMPIRICAL MODELING OF KINETICS OF TRANSESTERIFICATION AND COLD FLOW PROPERTIES OF USED SOYA OIL BIODIESEL

This research work focused on empirical modeling of kinetics of transesterification and cold flow properties of homogeneous catalyzed used soya oil fatty acid methyl ester (USOFAME]. Used soya oil (USO) was prepared by frying food (yam, potato plantain etc) with virgin soya oil for a total of 72 hours [1]. The oil was characterized based on American Society for Testing and Materials (ASTM) method. The fatty acid profile of used soya oil was analyzed using gas chromatography mass spectroscopy (GC MS) while the functional groups of the triglyceride were determined using Fourier transform infrared spectroscopy (FTIR). The oil was pretreated to reduce the free fatty acid level below 1% and then transesterified using methanol in the presence of sodium hydroxide catalyst. The fuel properties of the USOFAME produced were determined based on ASTM standards. Kinetic experiments were conducted in batches at different temperatures of 450C, 550C and 650C. Application of rate laws to the three-step reversible reaction scheme of transesterification yielded a series of ordinary differential equations (ODEs) solved with polymath 5.1 software to give the forward and reverse rate constants k1,k2, k3, k4, k5 and k6 from which the rate limiting step (RLS) and activation energy (∆E) were derived. The cold flow properties, cloud point (CP), cold filter plugging point (CFPP) and pour point (PP) were determined experimentally for different blends of biodiesel with #2 diesel, at a percentage volume ratio of biodiesel to diesel 0, 20, 40, 60, 80, and 100. The values obtained for CP, CFPP, and PP were plotted against the biodiesel fraction in the blends. Least square regression of the data of the plots were tested on linear, quadratic and polynomial models using Microsoft excel. The fuel properties of the USOFAME which is within the ASTM standards were determined as acid value 0.4mgKOH/g, density 863mm2/s, kinematic viscosity 4.60mm2/s, flash point 1620C, cetane number 61.00, calorific value 40.06MJ/Kg, pour point -40C, cold filter plugging point -2.80C, cloud point 00C, iodine value 30.60gI2/100g. Kinetic modeling of transesterification of USOFAME shows that the forward rate constants K1, K2, and K3 are greater than those of the reverse reaction k2, k4, k6, imply that the forward reaction dominates while the reverse reaction could be neglected. The rate constant k1 for triglyceride conversion to diglyceride is the least among the forward rate constants at 450C, 550C and650C imply that this step is the rate limiting step (RLS). Application of least square regression analysis of Microsoft excel on the data of variation of cold flow properties with biodiesel fraction, revealed polynomial model to be the best fitting equation.

Quantification and Prediction of Imine Formation Kinetics in Aqueous Solution by Microfluidic NMR Spectroscopy.

Quantitatively predicting the reactivity of dynamic covalent reaction is essential to understand and rationally design complex structures and reaction networks. Herein, the reactivity of aldehydes and amines in various rapid imine formation in aqueous solution by microfluidic NMR spectroscopy was quantified. Investigation of reaction kinetics allowed to quantify the forward rate constants k+ by an empirical equation, of which three independent parameters were introduced as reactivity parameters of aldehydes (SE , E) and amines (N). Furthermore, these reactivity parameters were successfully used to predict the unknown forward rate constants of imine formation. Finally, two competitive reaction networks were rationally designed based on the proposed reactivity parameters. Our work has demonstrated the capability of microfluidic NMR spectroscopy in quantifying the kinetics of label-free chemical reactions, especially rapid reactions that are complete in minutes.

Dopamine D2 Receptor Agonist Binding Kinetics-Role of a Conserved Serine Residue.

The forward (kon) and reverse (koff) rate constants of drug–target interactions have important implications for therapeutic efficacy. Hence, time-resolved assays capable of measuring these binding rate constants may be informative to drug discovery efforts. Here, we used an ion channel activation assay to estimate the kons and koffs of four dopamine D2 receptor (D2R) agonists; dopamine (DA), p-tyramine, (R)- and (S)-5-OH-dipropylaminotetralin (DPAT). We further probed the role of the conserved serine S1935.42 by mutagenesis, taking advantage of the preferential interaction of (S)-, but not (R)-5-OH-DPAT with this residue. Results suggested similar koffs for the two 5-OH-DPAT enantiomers at wild-type (WT) D2R, both being slower than the koffs of DA and p-tyramine. Conversely, the kon of (S)-5-OH-DPAT was estimated to be higher than that of (R)-5-OH-DPAT, in agreement with the higher potency of the (S)-enantiomer. Furthermore, S1935.42A mutation lowered the kon of (S)-5-OH-DPAT and reduced the potency difference between the two 5-OH-DPAT enantiomers. Kinetic Kds derived from the koff and kon estimates correlated well with EC50 values for all four compounds across four orders of magnitude, strengthening the notion that our assay captured meaningful information about binding kinetics. The approach presented here may thus prove valuable for characterizing D2R agonist candidate drugs.

Redox Cycling within Nanoparticle-Nucleated Protein Superstructures: Electron Transfer between Nanoparticulate Gold, Molecular Reductant, and Cytochrome c.

We previously described how thousands of the heme protein cytochrome c (cyt.c) self-organize into multilayered, roughly spherical superstructures as initiated by nucleation around one colloidal gold or silver nanoparticle. Within these superstructures, the protein is stabilized to unfolding in buffered media and survives superstructure encapsulation within silica gels and processing to form bioaerogels. We now report that Au∼cyt.c superstructures in buffered media are not simply static groupings of proteins, but that the Au core and protein corona exhibit dynamic electron-transfer reactions within the superstructure as verified by UV-visible and resonance Raman spectroscopy. Within the superstructure, hundreds to thousands of ferricytochrome c (FeIII-cyt.c) are reduced to ferrocytochrome c (FeII-cyt.c) following first-order kinetics with an average apparent forward rate constant of 1.9 ±0.4 × 10-5 s-1. The reducing power in the microheterogeneous medium is derived from two multielectron reductants: tannic acid used to stabilize the commercial gold sol and the Au nanoparticle at the center of the protein superstructure. Fluorescence monitoring of guanidinium chloride-induced unfolding reveals that superstructure-associated cyt.c is stabilized to unfolding before and after chemical reduction of FeIII-cyt.c to form FeII-cyt.c, indicating that the superstructures remain intact during microheterogeneous redox reactions. Smaller nucleating Au nanoparticles or lower ionic strength in the buffered medium yields a greater extent of cyt.c reduction. Partial oxidation of the cyt.c-associated nanoparticulate Au is verified by X-ray photoelectron spectroscopy. The Au nanoparticle at the heart of the superstructure functions as a direct electron donor to the heme with oxidized Au atoms being recycled back to Au(0) as long as residual tannic acid, derived from the Au sol mother liquor, is present in the aqueous microheterogeneous medium.

Kinetic studies on esterification of acetic acid with isopropyl alcohol in presence of novel solid catalyst

Abstract The reaction of isopropyl alcohol with acetic acid was carried out in an isothermal batch reactor in presence of solid resin catalyst to produce isopropyl acetate and water. A novel solid resin catalyst Indion 140 was used in the present study. The temperature of reaction mixture was maintained in the range of 333.15 – 363.15 K. The effects of reaction temperature, catalyst loading, mole ratio, size of catalyst, agitation speed were investigated on acetic acid conversion. Further, pseudo-homogeneous kinetic model was developed for the catalyzed reaction. The forward reaction rate constants and activation energies were determined from the Arrhenius plot. The forward and backward activation energies are found to 53,459 J/mol and 54,748 J/mol, respectively. The heat of reaction is −1.289 kJ/mol with Indion 140 catalyst. The mathematical equation was developed for frequency factor as function of the catalyst loading and found that it follows a linear relationship between frequency factor and catalyst loading. The simulations were performed for pseudo homogeneous kinetic model and found that the model is able to predict the experimental data very well. The developed kinetic equation is useful for the simulation of a reactive distillation column for the synthesis of isopropyl acetate.

Three-Coordinate Zinc Methyl Complexes with Sterically Demanding Formazanate Ligands

A series of heteroleptic three-coordinate mono(formazanate)zinc methyl complexes were synthesized, and the influence of the ligand on the structure as well as redox and optical properties of these complexes was investigated. The heteroleptic mono(formazanate)zinc methyl complexes were found to show ligand redistribution in solution, reminiscent of the Schlenk equilibrium, to generate an equilibrium mixture containing the corresponding homoleptic complexes as well. Monitoring the approach to equilibrium by NMR spectroscopy in benzene-d(6) allowed determination of the forward and backward rate constants. A correlation was found between the steric environment around the zinc center and equilibrium concentration of (formazanate)zinc methyl compounds, whereas the kinetics for approach to equilibrium are also dependent on the electronic properties.

Effect of non-aqueous solvents on kinetics of carbon dioxide absorption by tBu3P/B(C6F5)3 frustrated Lewis pairs

Frustrated Lewis pairs (FLPs), combinations of sterically hindered Lewis acids and bases, are known for their ability to capture CO2. Although there have been several theoretical studies on the mechanisms of the reactions between CO2 and some FLP systems, experimental studies on the reaction kinetics have been inconclusive. In this study, the mechanism and kinetics of CO2 absorption by an FLP system consisting of tri-tert-butylphosphine (tBu3P) and tris(pentafluorophenyl)borane (B(C6F5)3) in bromobenzene, cyclopentyl methyl ether (CPME), and tert-butyl methyl ether (MTBE) were investigated using the stopped-flow method. The pseudo-first-order reaction rate constants, ko (s−1), were measured for a concentration range of 0.02–0.035 M and over a temperature range of 298–323 K. The experimental data were fitted according to modified termolecular mechanisms with average absolute relative deviations of 4.34%, 4.63%, and 3.51% for the CO2–FLP:bromobenzene, CO2–FLP:CPME, and CO2–FLP:MTBE systems, respectively. The forward reaction rate constants, k (m3 kmol−1 s−1), were calculated based on the proposed reaction mechanism. The forward reaction rate constants were higher than those for various aqueous tertiary amine systems but lower than those for aqueous monoethanolamine and piperazine systems. Moreover, the activation energies were estimated from Arrhenius plots. They were calculated to be 22.0, 19.7, and 21.8 kJ mol−1 for the CO2–FLP:bromobenzene, CO2–FLP:CPME, and CO2–FLP:MTBE systems, respectively. This study promotes the development of novel efficient solvent formulations for CO2 capture.

Reactivity of Polycyclic Aromatic Hydrocarbon Soot Precursors: Kinetics and Equilibria.

The thermodynamics and kinetics of cross-linking reactions between PAHs of various reactive edge types that are observed in soot precursors are explored using density functional theory. The forward rate constants confirm that reactions involving aryl σ-radicals are faster than others, but rate constants for reactions between aryl σ-radicals and localized π-radicals can be as large or even larger than for two aryl σ-radicals. However, rates for all cross-linking reactions between small PAHs are likely too slow to explain soot formation. The equilibrium constants show that reactions involving σ and π-radical PAHs are the most favorable at flame temperatures. Equilibrium constants for larger PAHs show that the ability to form bonded-and-stacked structures results in enhanced equilibrium constants for the reaction of two large localized π-radicals compared to those for other edge types. This suggests that combined physical and chemical interactions between larger π-radical PAHs could be important in flame environments.

Quantification of creatine kinase reaction rate in mouse hindlimb using phosphorus-31 magnetic resonance spectroscopic fingerprinting.

The goal of this study was to evaluate the accuracy, reproducibility, and efficiency of a 31 P magnetic resonance spectroscopic fingerprinting (31 P-MRSF) method for fast quantification of the forward rate constant of creatine kinase (CK) in mouse hindlimb. The 31 P-MRSF method acquired spectroscopic fingerprints using interleaved acquisition of phosphocreatine (PCr) and γATP with ramped flip angles and a saturation scheme sensitive to chemical exchange between PCr and γATP. Parameter estimation was performed by matching the acquired fingerprints to a dictionary of simulated fingerprints generated from the Bloch-McConnell model. The accuracy of 31 P-MRSF measurements was compared with the magnetization transfer (MT-MRS) method in mouse hindlimb at 9.4 T (n = 8). The reproducibility of 31 P-MRSF was also assessed by repeated measurements. Estimation of the CK rate constant using 31 P-MRSF (0.39 ± 0.03 s-1 ) showed a strong agreement with that using MT-MRS measurements (0.40 ± 0.05 s-1 ). Variations less than 10% were achieved with 2 min acquisition of 31 P-MRSF data. Application of the 31 P-MRSF method to mice subjected to an electrical stimulation protocol detected an increase in CK rate constant in response to stimulation-induced muscle contraction. These results demonstrated the potential of the 31 P-MRSF framework for rapid, accurate, and reproducible quantification of the chemical exchange rate of CK in vivo.

Accurate Rate Constants for the Forward and Reverse H + CO ↔ HCO Reactions at the High-Pressure Limit.

The forward and reverse H + CO ↔ HCO reactions are important for combustion chemistry and have been studied from a wide variety of theoretical and experimental techniques. However, most of the chemical kinetic investigations concerning these processes are focused on low pressures or fall-off regions. Hence, a high-level electronic structure treatment was employed here in order to provide accurate rate constant values for these reactions at the high-pressure limit along temperatures from 50 to 4000 K. In relative terms, the variational effects on rate constants are shown to be almost as important at high temperatures as quantum tunneling corrections at the lowest temperatures investigated. The activation energies fitted by using modified and traditional Arrhenius’ equations for the forward rate constants from 298 to 2000 K are, respectively, equal to 2.64 and 3.89 kcal mol–1, while similar fittings provided, respectively, 1.96 and 3.22 kcal mol–1, considering now forward rate constants from a temperature range of 298–373 K. This last activation energy determination (3.22 kcal mol–1) is in better agreement with the commonly referenced experimental value of 2.0 ± 0.4 kcal mol–1, also obtained from traditional fittings in the range 298–373 K, than the value attained from a broader temperature range fitting (3.89 kcal mol–1). However, some additional care must be considered along these comparisons once the experimental reaction rate measurements have been done for the trimolecular H + CO + M → HCO + M reaction instead. Anyway, the usage of appropriate temperature ranges is fundamental for reliable activation energy comparisons, although the remaining deviation between theory and experiment is still large and is possibly caused by the different pressure regimes assessed in each case. Finally, we roughly estimated that the high-pressure limit for the HCO decomposition into H and CO can be achieved along temperatures ranging from ∼246 and ∼255 K downward, respectively, at pressures of 1.1 and 9.6 atm, although further experiments should be carried out in order to improve these estimates. On the other hand, pressures larger than 9.8 × 104 atm are required for the aforementioned dissociation reaction to attain the high-pressure limit at 700 K. Therefore, the rate constants determined here are probably applicable in combustion studies at lower temperatures.

Prehydration and the Reversibility of Solid-State Hydrogen-Deuterium Exchange.

The reversibility of solid-state hydrogen-deuterium exchange (ssHDX) and the effects of prehydration on the rate and extent of deuterium incorporation were evaluated using poly-d,l-alanine (PDLA) peptides colyophilized with various excipients. In prehydration studies, samples were equilibrated at a controlled relative humidity (6% or 11% RH) for 12 h and then transferred to corresponding D2O humidity conditions (6% or 11% RD) for deuterium labeling. In amorphous samples, the rate and extent of deuterium incorporation were similar in prehydrated samples and controls not subjected to prehydration. In reversibility studies, PDLA samples were maximally deuterated in controlled D2O humidity conditions (6% or 11% RD) and then transferred to corresponding H2O relative humidity (0%, 6%, 11%, or 43% RH). Hysteresis in deuterium removal was observed when compared with the deuterium incorporation kinetics for all formulations and conditions, confirming that the reaction is reversible in the solid state and that the forward and reverse processes differ. The extent of deuterium loss reached a plateau that depended on the delabeling relative humidity. Reverse reaction rate constants were quantified using a first-order kinetic model, a limiting case of the reversible first-order model applicable under sink conditions. For other conditions, plateau (steady-state) deuteration levels were related to forward and reverse rate constants in a reversible first-order kinetic model. The results support a mechanistic interpretation of ssHDX kinetics as a reversible first-order process, in which the forward (deuteration) rate depends on the activity of the deuterium donor.

Real-Time Imaging of Intracellular Glutathione Levels Based on a Ratiometric Fluorescent Probe with Extremely Fast Response.

Glutathione (GSH), the most abundant nonprotein thiol found in living organisms, are involved in the etiology and progression of many human diseases including cancer. So, monitoring changes of cellular GSH levels has an important guiding significance. To date, however, majority of probes can only qualitatively detect GSH in living cells. Herein, with coumarin as the read-out fluorophore and Michael addition as the sensing mechanism, six fluorescent probes were designed and synthesized. Among them, RP-2 exhibited a reversible and extremely fast response toward GSH (half time: ∼3 s), which endowed RP-2 the capacity of real-time imaging. Among the reversible probes based on Michael addition, RP-2 had both the largest forward and reverse rate constants thus far. The reaction between RP-2 and GSH was studied in detail by density functional theory and fluorescence spectroscopy. Real-time imaging of GSH levels in living cells was achieved with a temporal resolution of seconds. To simplify the processing of images, a program was developed and validated. RP-2 was expected to serve as a new fluorescent imaging tool to understand the function of intracellular GSH in the future.

Differential Effects of Physiological Pyrophosphate on the Kinetics of Productive and Abortive Transcription Initiation

Transcription initiation is the first and most highly regulated step of gene expression, and a biophysical characterization of its mechanism is needed. Previous studies found two, roughly equal populations of DNA‐RNA open complexes (OCs) in transcription initiation: productive OC that escape from the promoter to make full length (FL) RNA and nonproductive OC that stall after synthesis of a short RNA, slowly release that RNA, and reinitiate (abortive initiation). The kinetics and mechanism of productive transcription initiation by E. coli RNA polymerase (RNAP) at the λPR promoter were recently determined without added pyrophosphate (PPi).1 Because each polymerization step of transcription releases PPi and total PPi concentrations in the cell are in the low mM range, it is important to determine the effects (e.g. product inhibition) of PPi on the catalytic and translocation steps of initiation, and compare with recent results for PPi effects on elongation.2 In the research reported here, we extend existing quantitative 32P‐detected initiation kinetic assays to physiological concentrations of PPi and assess PPi effects on both the amounts and rates of the steps of productive and abortive initiation. Using phosphorimager analysis of gel separations and one‐dimensional thin layer chromatography, we study single‐round initiation of FL RNA synthesis at RNAP‐λPR open complexes under conditions where overall forward rate constants for each step of NTP incorporation in hybrid extension up to and beyond the escape point (11bp for initiation from λPR promoter) were previously determined.1 This will allow determination of PPi effects on each step, and potentially a dissection into effects on translocation and catalytic steps. Results to date show distinct PPi effects on productive and nonproductive initiation. The level of FL RNA synthesis by productive complexes is significantly reduced, but the level of abortive initiation is increased, indicating that previously‐productive OC are stalled by PPi. An understanding of PPi effects on productive and abortive initiation is critical to future assessments of the regulation and fidelity of bacterial transcription initiation in vivo, and the in vivo significance of short abortive RNAs as regulators.