SciCombinator

Discover the most talked about and latest scientific content & concepts.

Concept: Collision theory

11

DNA walkers are designed with the structural specificity and functional diversity of oligonucleotides to actively convert chemical energy into mechanical translocation. Compared to natural protein motors, DNA walkers' small translocation distance (mostly <100 nm) and slow reaction rate (<0.1 nm s(-1)) make single-molecule characterization of their kinetics elusive. An important indication of single-walker kinetics is the rate-limiting reactions that a particular walker design bears. We introduce an integrated super-resolved fluorescence microscopy approach that is capable of long-term imaging to investigate the stochastic behavior of DNA walkers. Subdiffraction tracking and imaging in the visible and second near-infrared spectra resolve walker structure and reaction rates. The distributions of walker kinetics are analyzed using a stochastic model to reveal reaction randomness and the rate-limiting biochemical reaction steps.

Concepts: Nature, Collision theory, Stochastic process, Microscopy, Protein, Chemical kinetics, Chemical reaction, Reaction rate

6

Ozonolysis is a major tropospheric removal mechanism for unsaturated hydrocarbons and proceeds via “Criegee intermediates”–carbonyl oxides–that play a key role in tropospheric oxidation models. However, until recently no gas-phase Criegee intermediate had been observed, and indirect determinations of their reaction kinetics gave derived rate coefficients spanning orders of magnitude. Here, we report direct photoionization mass spectrometric detection of formaldehyde oxide (CH(2)OO) as a product of the reaction of CH(2)I with O(2). This reaction enabled direct laboratory determinations of CH(2)OO kinetics. Upper limits were extracted for reaction rate coefficients with NO and H(2)O. The CH(2)OO reactions with SO(2) and NO(2) proved unexpectedly rapid and imply a substantially greater role of carbonyl oxides in models of tropospheric sulfate and nitrate chemistry than previously assumed.

Concepts: Aldehyde, Collision theory, Chemical reaction, Ozonolysis, Oxygen, Reaction rate constant, Functional group, Reaction rate

5

The kinetics of the hydroxyl radical (OH) + carbon monoxide (CO) reaction, which is fundamental to both atmospheric and combustion chemistry, are complex because of the formation of the hydrocarboxyl radical (HOCO) intermediate. Despite extensive studies of this reaction, HOCO has not been observed under thermal reaction conditions. Exploiting the sensitive, broadband, and high-resolution capabilities of time-resolved cavity-enhanced direct frequency comb spectroscopy, we observed deuteroxyl radical (OD) + CO reaction kinetics and detected stabilized trans-DOCO, the deuterated analog of trans-HOCO. By simultaneously measuring the time-dependent concentrations of the trans-DOCO and OD species, we observed unambiguous low-pressure termolecular dependence of the reaction rate coefficients for N2 and CO bath gases. These results confirm the HOCO formation mechanism and quantify its yield.

Concepts: Oxygen, Collision theory, Hydroxyl radical, Carbon dioxide, Chemical reaction, Chemical kinetics, Reaction rate constant, Reaction rate

2

The role of artificially created defects and steps in the local reaction kinetics of CO oxidation on the individual domains of a polycrystalline Pd foil was studied by photoemission electron microscopy (PEEM), mass spectroscopy (MS), and scanning tunneling microscopy (STM). The defects and steps were created by STM-controlled Ar(+) sputtering and the novel PEEM-based approach allowed the simultaneous determination of local kinetic phase transitions on differently oriented μm-sized grains of a polycrystalline sample. The independent (single-crystal-like) reaction behavior of the individual Pd(hkl) domains in the 10(-5) mbar pressure range changes upon Ar(+) sputtering to a correlated reaction behavior, and the reaction fronts propagate unhindered across the grain boundaries. The defect-rich surface shows also a significantly higher CO tolerance as reflected by the shift of both the global (MS-measured) and the local (PEEM-measured) kinetic diagrams toward higher CO pressure.

Concepts: Collision theory, Scanning probe microscopy, Microscopy, Novel, Fundamental physics concepts, Electron microscope, Electron, Scanning tunneling microscope

1

Alterations in glutathione (GSH) homeostasis are associated with a variety of diseases and cellular functions, and therefore, real-time live-cell imaging and quantification of GSH dynamics are important for understanding pathophysiological processes. However, existing fluorescent probes are unsuitable for these purposes due to their irreversible fluorogenic mechanisms or slow reaction rates. In this work, we have successfully overcome these problems by establishing a design strategy inspired by Mayr’s work on nucleophilic reaction kinetics. The synthesized probes exhibit concentration-dependent, reversible and rapid absorption/fluorescence changes (t1/2 = 620 ms at [GSH] = 1 mM), as well as appropriate Kd values (1-10 mM: within the range of intracellular GSH concentrations). We also developed FRET-based ratiometric probes, and demonstrated that they are useful for quantifying GSH concentration in various cell types and also for real-time live-cell imaging of GSH dynamics with temporal resolution of seconds.

Concepts: Cellular manufacturing, Reaction rate constant, Design, Enzyme kinetics, Collision theory, Force, Chemical kinetics, Reaction rate

1

The mechanistic description of enzyme kinetics in a dynamic model of metabolism requires specifying the numerical values of a large number of kinetic parameters. The parameterization challenge is often addressed through the use of simplifying approximations to form reaction rate laws with reduced numbers of parameters. Whether such simplified models can reproduce dynamic characteristics of the full system is an important question.

Concepts: Metabolism, Chemical reaction, Rate equation, Number, Mathematics, Collision theory, Chemical kinetics, Reaction rate

0

Kinetic theory and thermodynamics of reaction networks are extended to the out-of-equilibrium dynamics of continuous-flow stirred tank reactors (CSTR) and serial transfers. On the basis of their stoichiometry matrix, the conservation laws and the cycles of the network are determined for both dynamics. It is shown that the CSTR and serial transfer dynamics are equivalent in the limit where the time interval between the transfers tends to zero proportionally to the ratio of the fractions of fresh to transferred solutions. These results are illustrated with a finite cross-catalytic reaction network and an infinite reaction network describing mass exchange between polymers. Serial transfer dynamics is typically used in molecular evolution experiments in the context of research on the origins of life. The present study is shedding a new light on the role played by serial transfer parameters in these experiments.

Concepts: Topology, Ratio, Present, Collision theory, Physics, Chemical reactor, Fundamental physics concepts, Time

0

In the current study, the thermodynamics of the slag-metal equilibrium reaction between Inconel 718 Ni-based alloy and CaF2-CaO-Al2O3-MgO-TiO2electroslag remelting (ESR)-type slags were systematically investigated in the temperature range from 1773 to 1973 K (1500 to 1700 °C). The equilibrium Al content increased with increasing temperature, whereas the equilibrium Ti content decreased with increasing temperature at a fixed slag composition. The important factors for controlling the oxidation of Al and Ti in the Inconel 718 superalloy were TiO2 > Al2O3 > CaO > CaF2 > MgO in ESR-type slag and Al > Ti in a consumable electrode. The conventional method of sampling by means of a quartz tube could result in contamination of the molten metal and changes in the size of the “special reaction interface”. Therefore, a novel method was used in the present study to investigate the slag-metal reaction kinetics to accurately obtain the kinetic parameters. The mass transfer coefficient was determined by coupling with the kinetic model derived from the assumption that the reaction rate ([Al] + (TiO2) = [Ti] + (Al2O3)) was controlled by the mass transfer of [Ti], [Al], (TiO2) and (Al2O3) in the boundary layer, respectively.

Concepts: Collision theory, Chemical engineering, Chemical reaction, Iron, Oxide, Reaction rate, Temperature, Thermodynamics

0

The process characteristics of microwave assisted hydrothermal carbonization of cellulose was investigated and a first order kinetics model based on carbon concentration was developed. Chemical properties analysis showed that comparing to conventional hydrothermal carbonization, hydrochar with comparable energy properties can be obtained with 5-10 times decrease in reaction time with assistance of microwave heating. Results from kinetics study was in great agreement with experimental analysis, that they both illustrated the predominant mechanism of the reaction depend on variations in the reaction rates of two co-existent pathways. Particularly, the pyrolysis-like intramolecular dehydration reaction was proved to be the predominant mechanism for hydrochar generation under high temperatures. Finally, the enhancement effects of microwave heating were reflected under both soluble and solid pathways in this research, suggesting microwave-assisted hydrothermal carbonization as a more attracting method for carbon-enriched hydrochar recovery.

Concepts: Temperature, Chemistry, Collision theory, Chemical kinetics, Microwave oven, Rate equation, Reaction rate, Chemical reaction

0

Diacylglycerol (DAG) and monoacylglycerol (MAG) are two natural occurring minor components found in most edible fats and oils. These compounds have gained increasing market demand owing to their unique physicochemical properties. Enzymatic glycerolysis in solvent-free system might be a promising approach in producing DAG and MAG-enriched oil. Understanding on glycerolysis mechanism is therefore of great importance for process simulation and optimization. In this study, a commercial immobilized lipase (Lipozyme TL IM) was used to catalyze the glycerolysis reaction. The kinetics of enzymatic glycerolysis reaction between triacylglycerol (TAG) and glycerol (G) were modeled using rate equation with unsteady-state assumption. Ternary complex, ping-pong bi-bi and complex ping-pong bi-bi models were proposed and compared in this study. The reaction rate constants were determined using non-linear regression and sum of square errors (SSE) were minimized. Present work revealed satisfactory agreement between experimental data and the result generated by complex ping-pong bi-bi model as compared to other models. The proposed kinetic model would facilitate understanding on enzymatic glycerolysis for DAG and MAG production and design optimization of a pilot-scale reactor.

Concepts: Collision theory, Chemical kinetics, Chemical reaction, Fat, Physical chemistry, Lipid, Reaction rate, Reaction rate constant