Reaction Time Scale Research Articles

On the origin of mode- and bond-selectivity in vibrationally mediated reactions on surfaces

The experimental observations of vibrational mode- and bond-selective chemistry at the gas-surface interface indicate that energy redistribution within the reaction complex is not statistical on the timescale of reaction. Such behavior is a key prerequisite for efforts to use selective vibrational excitation to control chemistry at the technologically important gas-surface interface. This paper outlines a framework for understanding the origin of non-statistical reactivity on surfaces. The model focuses on the kinetic competition between intramolecular vibrational energy redistribution (IVR) within the reaction complex, which in the long-time limit leads to statistical behavior, and quenching, scattering, or desorption processes that restrict the extent of IVR prior to reaction. Characteristic timescales for these processes drawn from studies of vibrational energy flow dynamics on surfaces and in the gas and condensed phases suggest that IVR is severely limited for important classes of surface reactions. Under these conditions, selective vibrational excitation can lead to preferential transition state access and result in mode- or bond-selective chemistry, even at high collision energies above the barrier to reaction. In addition to providing a basis for understanding experimental observations, the model provides guidance for identifying other gas-surface reactions that may exhibit mode-selective behavior.

A new method for the nitrosation of 1,3-diketones applied to 3-ethyl- and 3-methyl pentane-2,4-dione

The nitrosation of 3-ethylpentane-2,4-dione (EPD) and 3-methylpentane-2,4-dione (MPD) has been performed in aqueous acid medium following a new procedure for sample preparation. The two reagents, diketone and sodium nitrite, were mixed together in alkaline medium to give the corresponding enolate (E−) and nitrite ion (NO2−). The enol nitrosation reaction starts after acidifying the reaction medium. Different experimental conditions were tested in order to adapt the reaction time scale to conventional or stopped-flow UV-vis spectrophotometry. The objectives of this study were to demonstrate that the decomposition of nitrous acid is negligible in the time scale of the nitrosation reaction and to corroborate the published reaction mechanism for the nitrosation of some 3-substituted diketones that it was assumed to proceed through a chelate nitrosyl intermediate. The results were compared with that obtained when the last reagent, normally the ketone, was added over an acid mixture of the rest of the reactants, that is, the protocol followed in previously published studies.

A simple shape-controlled synthesis of gold nanoparticles using nonionic surfactants

Green and simple synthesis strategies have gained tremendous popularity for the production of anisotropically-shaped noble metallic nanoparticles. The long-term stability of the produced particles, the short timescale of the target reaction(s), as well as the use of non-toxic chemicals, are pivotal features of a useful green procedure. Herein we describe a simple and convenient wet-chemical approach to synthesize stable, non-toxic and water-soluble small gold nanotriangles (GNTs) and gold nanospheres (GNSs) in one step at room temperature, using Tween 20 and Tween 80, respectively. A high level of purity and monodispersity was obtained for the GNTs, in addition to an excellent colloidal stability of both GNTs and GNSs in media exhibiting a high ionic strength and over a wide pH range. The presented strategy, which exploits the dual functional properties of Tween as a co-reducing and stabilizing agent, eliminates the presence of hazardous chemicals such as toxic surfactants, hazardous organic solvents and harsh reducing agents during the synthesis process, and hence could pave the way for the facile usage of the spherical and triangular gold nanoparticles for clinical or biological applications. The resulted particles were characterized by UV-Vis spectroscopy, dynamic light scattering and transmission electron microscopy.

Microfluidic barcode assay for antibody-based confirmatory diagnostics

Confirmatory diagnostics offer high clinical sensitivity and specificity typically by assaying multiple disease biomarkers. Employed in clinical laboratory settings, such assays confirm a positive screening diagnostic result. These important multiplexed confirmatory assays require hours to complete. To address this performance gap, we introduce a simple 'single inlet, single outlet' microchannel architecture with multiplexed analyte detection capability. A streptavidin-functionalized, channel-filling polyacrylamide gel in a straight glass microchannel operates as a 3D scaffold for a purely electrophoretic yet heterogeneous immunoassay. Biotin and biotinylated capture reagents are patterned in discrete regions along the axis of the microchannel resulting in a barcode-like pattern of reagents and spacers. To characterize barcode fabrication, an empirical study of patterning behaviour was conducted across a range of electromigration and binding reaction timescales. We apply the heterogeneous barcode immunoassay to detection of human antibodies against hepatitis C virus and human immunodeficiency virus antigens. Serum was electrophoresed through the barcode patterned gel, allowing capture of antibody targets. We assess assay performance across a range of Damkohler numbers. Compared to clinical immunoblots that require 4-10 h long sample incubation steps with concomitant 8-20 h total assay durations; directed electromigration and reaction in the microfluidic barcode assay leads to a 10 min sample incubation step and a 30 min total assay duration. Further, the barcode assay reports clinically relevant sensitivity (25 ng ml(-1) in 2% human sera) comparable to standard HCV confirmatory diagnostics. Given the low voltage, low power and automated operation, we see the streamlined microfluidic barcode assay as a step towards rapid confirmatory diagnostics for a low-resource clinical laboratory setting.

Urban street canyons: Coupling dynamics, chemistry and within-canyon chemical processing of emissions

Street canyons, formed by rows of buildings in urban environments, are associated with high levels of atmospheric pollutants emitted primarily from vehicles, and substantial human exposure. The street canyon forms a semi-enclosed environment, within which emissions may be entrained in a re-circulatory system; chemical processing of emitted compounds alters the composition of the air vented to the overlying boundary layer, compared with the primary emissions. As the prevailing atmospheric chemistry is highly non-linear, and the canyon mixing and predominant chemical reaction timescales are comparable, the combined impacts of dynamics and chemistry must be considered to quantify these effects. Here we report a model study of the coupled impacts of dynamical and chemical processing upon the atmospheric composition in a street canyon environment, to assess the impacts upon air pollutant levels within the canyon, and to quantify the extent to which within-canyon chemical processing alters the composition of canyon outflow, in comparison to the primary emissions within the canyon. A new model for the simulation of street canyon atmospheric chemical processing has been developed, by integrating an existing Large-Eddy Simulation (LES) dynamical model of canyon atmospheric motion with a detailed chemical reaction mechanism, a Reduced Chemical Scheme (RCS) comprising 51 chemical species and 136 reactions, based upon a subset of the Master Chemical Mechanism (MCM). The combined LES–RCS model is used to investigate the combined effects of mixing and chemical processing upon air quality within an idealised street canyon. The effect of the combination of dynamical (segregation) and chemical effects is determined by comparing the outputs of the full LES–RCS canyon model with those obtained when representing the canyon as a zero-dimensional box model (i.e. assuming mixing is complete and instantaneous). The LES–RCS approach predicts lower (canyon-averaged) levels of NOx, OH and HO2, but higher levels of O3, compared with the box model run under identical chemical and emissions conditions. When considering the level of chemical detail implemented, segregation effects were found to reduce the error introduced by simplifying the reaction mechanism. Chemical processing of emissions within the canyon leads to a significant increase in the Ox flux from the canyon into the overlying boundary layer, relative to primary emissions, for the idealised case considered here. These results demonstrate that within-canyon atmospheric chemical processing can substantially alter the concentrations of pollutants injected into the urban canopy layer, compared with the raw emission rates within the street canyon. The extent to which these effects occur is likely to be dependent upon the nature of the domain (canyon aspect ratio), prevailing meteorology and emission/pollution scenario considered.

A Remote Mutation Affects the Hydride Transfer by Disrupting Concerted Protein Motions in Thymidylate Synthase

The role of protein flexibility in enzyme-catalyzed activation of chemical bonds is an evolving perspective in enzymology. Here we examine the role of protein motions in the hydride transfer reaction catalyzed by thymidylate synthase (TSase). Being remote from the chemical reaction site, the Y209W mutation of Escherichia coli TSase significantly reduces the protein activity, despite the remarkable similarity between the crystal structures of the wild-type and mutant enzymes with ligands representing their Michaelis complexes. The most conspicuous difference between these two crystal structures is in the anisotropic B-factors, which indicate disruption of the correlated atomic vibrations of protein residues in the mutant. This dynamically altered mutant allows a variety of small thiols to compete for the reaction intermediate that precedes the hydride transfer, indicating disruption of motions that preorganize the protein environment for this chemical step. Although the mutation causes higher enthalpy of activation of the hydride transfer, it only shows a small effect on the temperature dependence of the intrinsic KIE, suggesting marginal changes in the geometry and dynamics of the H-donor and -acceptor at the tunneling ready state. These observations suggest that the mutation disrupts the concerted motions that bring the H-donor and -acceptor together during the pre- and re-organization of the protein environment. The integrated structural and kinetic data allow us to probe the impact of protein motions on different time scales of the hydride transfer reaction within a complex enzymatic mechanism.

A kinetic model for H2 production by plasmolysis of water vapours at atmospheric pressure in a dielectric barrier discharge microchannel reactor

Abstract A kinetic model has been developed for water vapour dissociation flowing at atmospheric pressure under nonthermal plasma conditions and analysed for different pathways of water dissociation, reaction time scales and key kinetic steps for H 2 production. A stream of pure water vapour was considered. Different pathways of decomposition such as, dissociation reactions, electron dissociative attachment, dissociative ionisation reactions, ionisation reactions and dissociative excitation reactions were included along with other pathways for different species produced and consumed with in plasmolysis. Dissociation reaction was found to dominate the water vapour plasmolysis followed by electron dissociative attachment reaction being the other important kinetic step. Reaction time scales and concentration were found to be in direct relation with electron density and reached their respective highest values (concentration of H 2 , C H 2 = 16 moles/m 3 and τ reaction ≅ 10 −2 s) at maximum electron density (10 21 m −3 ). The time scale for reaching 99% of hydrogen produced (steady state concentration of H 2 ) was found to be around 10 −2 s which showed H 2 could be produced utilising very little power in micro-plasma reactors, in agreement with published theory (Lozano-Parada JH, Zimmerman WB. The role of kinetics in the design of plasma microreactors. Chemical Engineering Science 2010; 65(17):4925–30). When the model was run as dissociative attachment pathway (Reaction (8)) being the primary reaction to break water vapour, concentration of H 2 was reduced from 16 moles/m 3 to 4 moles/m 3 . However, it additionally introduces the H − radicals into the system which subsequently control the production of H by electron detachment. A detailed analysis was done to find out the major steps influencing the overall kinetics of water vapour plasmolysis. Recombination reaction of H–H atoms was not found to be significant for the production of H 2 . The key step for the generation of H 2 was the reaction between H and HO 2 . Finally, a mechanism consistent with the kinetically important steps is proposed.

Application-Oriented Analysis of Mixing Performance in Microreactors

A methodology was developed to select adequate, commercially available micromixers for mixing sensitive chemical reactions. The range of flow rates can be derived at which the selected micromixers have to be operated to ensure the required mixing intensity. This methodology enables the selection of adequate micromixers for the scale up of the chemical reactions to higher flow rates. Two chemical test reactions were used for an experimental approach to characterize the selected microreactors. Both reactions are based on the effect of micromixing on the product distribution of competitive reaction systems. Flow rates and pressure drop were determined at which the mixing times are short relative to the reaction times. In this case, influences of mixing on the selectivity of the reference reaction can be neglected. Since two reference reactions with different time scales for mixing and reaction were tested, it was possible to study the mixing performance of a variety of micromixers over a wide range of flow rates. The investigated micromixers differ in their dimensions, internal geometry, and mixing principle. In the present work, overview tables are provided as a tool to evaluate the commercially available micromixers for specific applications. Further, the influence of mixing principle and pressure drop is discussed.

MESMER: An Open-Source Master Equation Solver for Multi-Energy Well Reactions

The most commonly used theoretical models for describing chemical kinetics are accurate in two limits. When relaxation is fast with respect to reaction time scales, thermal transition state theory (TST) is the theoretical tool of choice. In the limit of slow relaxation, an energy resolved description like RRKM theory is more appropriate. For intermediate relaxation regimes, where much of the chemistry in nature occurs, theoretical approaches are somewhat less well established. However, in recent years master equation approaches have been successfully used to analyze and predict nonequilibrium chemical kinetics across a range of intermediate relaxation regimes spanning atmospheric, combustion, and (very recently) solution phase organic chemistry. In this article, we describe a Master Equation Solver for Multi-Energy Well Reactions (MESMER), a user-friendly, object-oriented, open-source code designed to facilitate kinetic simulations over multi-well molecular energy topologies where energy transfer with an external bath impacts phenomenological kinetics. MESMER offers users a range of user options specified via keywords and also includes some unique statistical mechanics approaches like contracted basis set methods and nonadiabatic RRKM theory for modeling spin-hopping. It is our hope that the design principles implemented in MESMER will facilitate its development and usage by workers across a range of fields concerned with chemical kinetics. As accurate thermodynamics data become more widely available, electronic structure theory is increasingly reliable, and as our fundamental understanding of energy transfer improves, we envision that tools like MESMER will eventually enable routine and reliable prediction of nonequilibrium kinetics in arbitrary systems.

Biomixing by chemotaxis and efficiency of biological reactions: The critical reaction case

Many phenomena in biology involve both reactions and chemotaxis. These processes can clearly influence each other, and chemotaxis can play an important role in sustaining and speeding up the reaction. In continuation of our work [A. Kiselev and L. Ryzhik, “Biomixing by chemotaxis and enhancement of biological reactions,” Comm. Partial Differential Equations 37, 298–318 (2012)]10.1080/03605302.2011.589879, we consider a model with a single density function involving diffusion, advection, chemotaxis, and absorbing reaction. The model is motivated, in particular, by the studies of coral broadcast spawning, where experimental observations of the efficiency of fertilization rates significantly exceed the data obtained from numerical models that do not take chemotaxis (attraction of sperm gametes by a chemical secreted by egg gametes) into account. We consider the case of the weakly coupled quadratic reaction term, which is the most natural from the biological point of view and was left open in Kiselev and Ryzhik [“Biomixing by chemotaxis and enhancement of biological reactions,” Comm. Partial Differential Equations 37, 298–318 (2012)]10.1080/03605302.2011.589879. The result is that similarly to Kiselev and Ryzhik [“Biomixing by chemotaxis and enhancement of biological reactions,” Comm. Partial Differential Equations 37, 298–318 (2012)]10.1080/03605302.2011.589879, the chemotaxis plays a crucial role in ensuring efficiency of reaction. However, mathematically, the picture is quite different in the quadratic reaction case and is more subtle. The reaction is now complete even in the absence of chemotaxis, but the timescales are very different. Without chemotaxis, the reaction is very slow, especially for the weak reaction coupling. With chemotaxis, the timescale and efficiency of reaction are independent of the coupling parameter.

THE RELATIONSHIP BETWEEN THE SUDDEN CHANGE OF THE LORENTZ FORCE AND THE MAGNITUDE OF ASSOCIATED FLARES

The rapid and irreversible change of photospheric magnetic fields associated with flares has been confirmed by many recent studies. These studies showed that the photospheric magnetic fields respond to coronal field restructuring and turn to a more horizontal state near the magnetic polarity inversion line (PIL) after eruptions. Recent theoretical work has shown that the change in the Lorentz force associated with a magnetic eruption will lead to such a field configuration at the photosphere. The Helioseismic Magnetic Imager has been providing unprecedented full-disk vector magnetograms covering the rising phase of the solar cycle 24. In this study, we analyze 18 flares in four active regions, with GOES X-ray class ranging from C4.7 to X5.4. We find that there are permanent and rapid changes of magnetic field around the flaring PIL, the most notable of which is the increase of the transverse magnetic field. The changes of fields integrated over the area and the derived change of Lorentz force both show a strong correlation with flare magnitude. It is the first time that such magnetic field changes have been observed even for C-class flares. Furthermore, for seven events with associated CMEs, we use an estimate of the impulse provided by the Lorentz force, plus the observed CME velocity, to estimate the CME mass. We find that if the time scale of the back reaction is short, i.e., in the order of 10 s, the derived values of CME mass (10^{15} g) generally agree with those reported in literature.

A Molecular Line Survey of CRL 2688 at 1 mm and 3 mm Wavelengths

AbstractIt is well established that circumstellar envelopes (CSEs) around evolved stars are active sites of molecular synthesis, and CSEs are one of the major sources of chemical enrichment in the interstellar space. The investigation of molecular compositions in CSEs is essential to understand the chemical evolution of the Galaxy. In order to study circumstellar chemistry in different environments, we have been systematically performing molecular line surveys of a sample of evolved stars from asymptotic giant branch (AGB) stars, proto-planetary nebulae (PPNs), to planetary nebulae (PNs). The dynamical time scales in different evolutionary stages can impose a time limit on the reaction time scales. Here we report our results for CRL 2688.

URDME: a modular framework for stochastic simulation of reaction-transport processes in complex geometries.

BackgroundExperiments in silico using stochastic reaction-diffusion models have emerged as an important tool in molecular systems biology. Designing computational software for such applications poses several challenges. Firstly, realistic lattice-based modeling for biological applications requires a consistent way of handling complex geometries, including curved inner- and outer boundaries. Secondly, spatiotemporal stochastic simulations are computationally expensive due to the fast time scales of individual reaction- and diffusion events when compared to the biological phenomena of actual interest. We therefore argue that simulation software needs to be both computationally efficient, employing sophisticated algorithms, yet in the same time flexible in order to meet present and future needs of increasingly complex biological modeling.ResultsWe have developed URDME, a flexible software framework for general stochastic reaction-transport modeling and simulation. URDME uses Unstructured triangular and tetrahedral meshes to resolve general geometries, and relies on the Reaction-Diffusion Master Equation formalism to model the processes under study. An interface to a mature geometry and mesh handling external software (Comsol Multiphysics) provides for a stable and interactive environment for model construction. The core simulation routines are logically separated from the model building interface and written in a low-level language for computational efficiency. The connection to the geometry handling software is realized via a Matlab interface which facilitates script computing, data management, and post-processing. For practitioners, the software therefore behaves much as an interactive Matlab toolbox. At the same time, it is possible to modify and extend URDME with newly developed simulation routines. Since the overall design effectively hides the complexity of managing the geometry and meshes, this means that newly developed methods may be tested in a realistic setting already at an early stage of development.ConclusionsIn this paper we demonstrate, in a series of examples with high relevance to the molecular systems biology community, that the proposed software framework is a useful tool for both practitioners and developers of spatial stochastic simulation algorithms. Through the combined efforts of algorithm development and improved modeling accuracy, increasingly complex biological models become feasible to study through computational methods. URDME is freely available at http://www.urdme.org.

Electron Tunneling Pathways and Role of Adenine in Repair of Cyclobutane Pyrimidine Dimer by DNA Photolyase

Electron tunneling pathways in enzymes are critical to their catalytic efficiency. Through electron tunneling, photolyase, a photoenzyme, splits UV-induced cyclobutane pyrimidine dimer into two normal bases. Here, we report our systematic characterization and analyses of photoinitiated three electron transfer processes and cyclobutane ring splitting by following the entire dynamical evolution during enzymatic repair with femtosecond resolution. We observed the complete dynamics of the reactants, all intermediates and final products, and determined their reaction time scales. Using (deoxy)uracil and thymine as dimer substrates, we unambiguously determined the electron tunneling pathways for the forward electron transfer to initiate repair and for the final electron return to restore the active cofactor and complete the catalytic photocycle. Significantly, we found that the adenine moiety of the unusual bent flavin cofactor is essential to mediating all electron-transfer dynamics through a superexchange mechanism, leading to a delicate balance of time scales. The cyclobutane ring splitting takes tens of picoseconds, while electron-transfer dynamics all occur on a longer time scale. The active-site structural integrity, unique electron tunneling pathways, and the critical role of adenine ensure the synergy of these elementary steps in this complex photorepair machinery to achieve maximum repair efficiency which is close to unity. Finally, we used the Marcus electron-transfer theory to evaluate all three electron-transfer processes and thus obtained their reaction driving forces (free energies), reorganization energies, and electronic coupling constants, concluding that the forward and futile back-electron transfer is in the normal region and that the final electron return of the catalytic cycle is in the inverted region.

Scalable synthesis and photoelectrochemical properties of copper oxide nanowire arrays and films

Here, we present a scalable method based on both atmospheric plasma and wet chemical oxidation methods to synthesize thin films and nanowire arrays of both cupric and cuprous oxides. In terms of nanowire arrays, the wet chemical oxidation is shown to produce copper hydroxide nanowire arrays on copper foils using hydrogen peroxide as the oxidant similar to ammonium persulfate. Experiments using different concentrations of hydrogen peroxide at constant pH resulted in higher nucleation density and smaller diameter of copper hydroxide nanowires. A scheme involving a short period of wet oxidation followed by plasma annealing resulted in high number density of Cu2O nanowire arrays. The overall process is rapid on the order of 1min reaction time scale. Photoelectrochemical characterization of titania coated copper oxide nanowire and thin film electrodes showed that the nanowire array electrodes exhibited significantly higher photoactivity than the thin film electrodes. The performance of resulting Cu2O NW array electrodes can be optimized further with other protective coatings.

QUANTIZATION OF CHEMICAL REACTION: THE DYNAMIC CORRELATION DIAGRAM METHOD FREE FROM NONCROSSING RULE

Both Fukui's frontier orbital (FO) theory and Woodward–Hoffmann's orbital symmetry conservation (W–H) theory are based on the molecular orbital theory. However, there are some obvious inconsistencies between the two theories in explaining the electron movement. The process of chemical reactions has been explained by the potential surface analysis based on the time-independent Schrödinger equation. However, this approach is not always appropriate for describing unsteady states, because the variable of reaction coordinate should be time t by its very nature. When considering the time-scale of chemical reactions for molecules, there is inherent uncertainty in the energy levels for the midway state of chemical reactions owing to the Heisenberg uncertainty principle. The states which can be accurately described by quantum mechanics exist discontinuously in chemical reactions. Such quantization of chemical reactions solves all noncrossing problems. We also show that such an essential fact leads to new concepts and theories in chemical reactions such as stable molecule, elementary reaction and minimum deformation of orbital phases. Finally, taking the regularity in organic reactions as an example, we demonstrate that FO theory and W–H theory can be unified consistently by the universally applicable "dynamic correlation diagram method."

Synthesis and characterization of Magneli phases: Reduction of TiO2 in a decomposed NH3 atmosphere

The present work reports a method for preparing electrically conductive titanium suboxides materials of Magneli phases with relatively low temperature treatment and short reaction time scale. We successfully produced Ti4O7, Ti5O9 and Ti6O11 by reducing TiO2 in an instantaneously decomposed ammonia atmosphere at high temperature. The influences of reduction temperature and time to the reduced phases were revealed. Ti4O7 was obtained by annealing rutile TiO2 in the reductive atmosphere at 1323K for 3h. The morphology of the materials was characterized by a scanning electron microscope, and the SEM images clearly show the spherical and porous particles of the reduced sample. However, the BET surface area of the produced Ti4O7 material is 1.99m2·g−1, which is too low for application in electrocatalysis.

Replacement of olivine by serpentine in the carbonaceous chondrite Nogoya (CM2)

Coarse (chondrule and isolated) olivine in some CM chondrites is replaced by serpentine in both centripetal and meshwork replacement textures. Locally preserved textures formed by partial replacement of coarse olivine by serpentine in the carbonaceous chondrite Nogoya (CM2) establish unique associations between each individual mass of serpentine and the specific olivine from which that serpentine formed. Electron probe microanalyses show that the composition of serpentine replacing coarse olivine is uniform throughout all analyzed volumes of Nogoya, and is independent of the composition of the olivine being replaced. If, as previously proposed, late-stage alteration fluids were Mg-rich because Fe-source minerals were depleted in earlier stages, then the uniform Mg-rich composition of the serpentine replacing large silicate grains during advanced stages of alteration may indicate diffusional homogenization of the aqueous solutions over progressively larger spatial scales, enabled by long timescales and previously proposed stagnant or slow-moving fluids.The range of olivine compositions replaced in Nogoya is even larger than previously reported from ALH 81002 (CM2). This militates against hypotheses of strong primary-mineral control on the compositions of alteration products, at least at advanced stages of alteration. The serpentine formed by olivine replacement in Nogoya is more magnesian than the counterpart serpentine replacing all anhydrous primary silicates in ALH 81002. This intermeteorite heterogeneity of replacement-serpentine composition between ALH 81002 and Nogoya indicates that the aqueous solutions in which the olivine-serpentine replacement reactions occurred were of different compositions in the two different CM parent-body volumes sampled by ALH 81002 and Nogoya. The more magnesian character of serpentines in Nogoya than in ALH 81002 indicates that the Nogoya aqueous-alteration environment was even more highly evolved toward Mg-rich solutions than the environment indicated by the composition of the serpentine in ALH 81002.Persistence of primary-silicate remnants within centripetal and meshwork serpentine indicates that either the aqueous alteration episodes in the parent-body volumes represented by individual meteorites were too short to allow complete replacement of olivine by serpentine, or one or more reactants (most likely water) were completely consumed before the coarse primary silicate was completely replaced. Seemingly incompatible arguments for and against primary-mineral control of serpentine composition during CM chondrite alteration may be reconciled by considering the different grain sizes and reaction timescales that likely existed in different textural settings.

Numerical approximation of Turing patterns in electrodeposition by ADI methods

In this paper we study the numerical approximation of Turing patterns corresponding to steady state solutions of a PDE system of reaction–diffusion equations modeling an electrodeposition process. We apply the Method of Lines (MOL) and describe the semi-discretization by high order finite differences in space given by the Extended Central Difference Formulas (ECDFs) that approximate Neumann boundary conditions (BCs) with the same accuracy. We introduce a test equation to describe the interplay between the diffusion and the reaction time scales. We present a stability analysis of a selection of time-integrators (IMEX 2-SBDF method, Crank–Nicolson (CN), Alternating Direction Implicit (ADI) method) for the test equation as well as for the Schnakenberg model, prototype of nonlinear reaction–diffusion systems with Turing patterns. Eventually, we apply the ADI-ECDF schemes to solve the electrodeposition model until the stationary patterns (spots & worms and only spots) are reached. We validate the model by comparison with experiments on Cu film growth by electrodeposition.

Protein Dynamics Studied with Ultrafast Two-Dimensional Infrared Vibrational Echo Spectroscopy

Proteins, enzymes, and other biological molecules undergo structural dynamics as an intrinsic part of their biological functions. While many biological processes occur on the millisecond, second, and even longer time scales, the fundamental structural dynamics that eventually give rise to such processes occur on much faster time scales. Many decades ago, chemical kineticists focused on the inverse of the reaction rate constant as the important time scale for a chemical reaction. However, through transition state theory and a vast amount of experimental evidence, we now know that the key events in a chemical reaction can involve structural fluctuations that take a system of reactants to its transition state, the crossing of a barrier, and the eventual relaxation to product states. Such dynamics occur on very fast time scales. Today researchers would like to investigate the fast structural fluctuations of biological molecules to gain an understanding of how biological processes proceed from simple structural changes in biomolecules to the final, complex biological function. The study of the fast structural dynamics of biological molecules requires experiments that operate on the appropriate time scales, and in this Account, we discuss the application of ultrafast two-dimensional infrared (2D IR) vibrational echo spectroscopy to the study of protein dynamics. The 2D IR vibrational echo experiment is akin to 2D NMR, but it operates on time scales many orders of magnitude faster. In the experiments, a particular vibrational oscillator serves as a vibrational dynamics probe. As the structure of the protein evolves in time, the structural changes are manifested as time-dependent changes in the frequency of the vibrational dynamics probe. The 2D IR vibrational echo experiments can track the vibrational frequency evolution, which we then relate to the time evolution of the protein structure. In particular, we measured protein substate interconversion for mutants of myoglobin using 2D IR chemical exchange spectroscopy and observed well-defined substate interconversion on a sub-100 ps time scale. In another study, we investigated the influence of binding five different substrates to the enzyme cytochrome P450(cam). The various substrates affect the enzyme dynamics differently, and the observed dynamics are correlated with the enzyme's selectivity of hydroxylation of the substrates and with the substrate binding affinity.