Stochastic simulation of chemical reactions in spatially complex media

Discrete stochastic simulations, via techniques such as the Stochastic Simulation Algorithm (SSA) are a powerful tool for understanding the dynamics of chemical kinetics when there are low numbers of certain molecular species. However, an important constraint is the assumption of well-mixedness and homogeneity. In this paper, we show how to use Monte Carlo simulations to estimate an anomalous diffusion parameter that encapsulates the crowdedness of the spatial environment. We then use this parameter to replace the rate constants of bimolecular reactions by a time-dependent power law to produce an SSA valid in cases where anomalous diffusion occurs or the system is not well-mixed (ASSA). Simulations then show that ASSA can successfully predict the temporal dynamics of chemical kinetics in a spatially constrained environment.

Relaxation Time of Chemical Reactions from Network Thermodynamics

The relationship for the relaxation time(s) of a chemical reaction in terms of concentrations and rate constants has been derived from the network thermodynamic approach developed by Oster, Perelson, and Katchalsky.Generally, it is necessary to draw the bond graph and the “network analogue” of the reaction scheme, followed by loop or nodal analysis of the network and finally solving of the resulting differential equations. In the case of single-step reactions, however, it is possible to obtain an expression for the relaxation time. This approach is simpler and elegant and has certain advantages over the usual kinetic method. The method has been illustrated by taking different reaction schemes as examples.

Modeling of Freezing Phenomena Induced by Chemical Reactions

Spatial variations in the concentration of a reactive solute in solution are often encountered in a catalyst particle, and this leads to variation in the freezing point of the solution. Depending on the operating temperature, this can result in freezing of the solvent oil a portion of catalyst, rendering that part of the active area ineffective Freezing call occur by formation of a sharp front or it mush that separates the solid and fluid phases. In this paper, we model the extent of reduction in the active area due to freezing. Assuming that the freezing point decreases linearly with solute concentration, conditions for freezing to occur have been derived. At steady state, the ineffective fraction of catalyst pellet is found to be the same irrespective of the mode of freezing. Progress of freezing is determined by both the heat of reaction and the latent heat of fusion Unlike in freezing of alloys where the latter plays a dominant role, the exothermicity of the reaction has a significant effect on freezing in the presence of chemical reactions. A dimensionless group analogous to the Stefan number could be defined to capture the combined effect of both of these.

Dynamics of Barrierless and Activated Chemical Reactions in a Dispersive Medium within the Fractional Diffusion Equation Approach

Barrierless chemical reactions have often been modeled as a Brownian motion on a one-dimensional harmonic potential energy surface with a position-dependent reaction sink or window located near the minimum of the surface. This simple (but highly successful) description leads to a nonexponential survival probability only at small to intermediate times but exponential decay in the long-time limit. However, in several reactive events involving proteins and glasses, the reactions are found to exhibit a strongly nonexponential (power law) decay kinetics even in the long time. In order to address such reactions, here, we introduce a model of barrierless chemical reaction where the motion along the reaction coordinate sustains dispersive diffusion. A complete analytical solution of the model can be obtained only in the frequency domain, but an asymptotic solution is obtained in the limit of long time. In this case, the asymptotic long-time decay of the survival probability is a power law of the Mittag−Leffler functional form. When the barrier height is increased, the decay of the survival probability still remains nonexponential, in contrast to the ordinary Brownian motion case where the rate is given by the Smoluchowski limit of the well-known Kramers' expression. Interestingly, the reaction under dispersive diffusion is shown to exhibit strong dependence on the initial state of the system, thus predicting a strong dependence on the excitation wavelength for photoisomerization reactions in a dispersive medium. The theory also predicts a fractional viscosity dependence of the rate, which is often observed in the reactions occurring in complex environments.

Nanocomposite based flexible ultrasensitive resistive gas sensor for chemical reactions studies

Room temperature operation, low detection limit and fast response time are highly desirable for a wide range of gas sensing applications. However, the available gas sensors suffer mainly from high temperature operation or external stimulation for response/recovery. Here, we report an ultrasensitive-flexible-silver-nanoparticle based nanocomposite resistive sensor for ammonia detection and established the sensing mechanism. We show that the nanocomposite can detect ammonia as low as 500 parts-per-trillion at room temperature in a minute time. Furthermore, the evolution of ammonia from different chemical reactions has been demonstrated using the nanocomposite sensor as an example. Our results demonstrate the proof-of-concept for the new detector to be used in several applications including homeland security, environmental pollution and leak detection in research laboratories and many others.

One possible way to promote the bond-selective chemical-reactions by frequency-modulated lasers

It is proposed in this paper that we can use frequency-modulated (FM) lasers to realize bond-selective chemical reactions or to raise the efficiency of molecular isotope separation. Examples are given for HF molecule and the C–H bond in some hydrocarbons.

Joint research project on the aquatic ecotoxicity of organo-aluminium: Chemical reactions. First interim report

The overall goal of the joint research project is to relate the chemical reactions involved in the formation of organo-aluminium complexes under acid conditions to their toxic effects on the physiology of aquatic organisms. Finally, this research is intended to predict toxic effects arising from acidity and aluminium under varying environmental conditions. This interim report examines the chemical modelling of ion-binding by humic substances where a computer model has been developed and is being tested using field data, and conditions required for the precipitation of aluminium in surface waters.

Topologically invariant reaction coordinates for simulating multistate chemical reactions.

Evaluating free energy profiles of chemical reactions in complex environments such as solvents and enzymes requires extensive sampling, which is usually performed by potential of mean force (PMF) techniques. The reliability of the sampling depends not only on the applied PMF method but also the reaction coordinate space within the dynamics is biased. In contrast to simple geometrical collective variables that depend only on the positions of the atomic coordinates of the reactants, the E(gap) reaction coordinate (the energy difference obtained by evaluating a suitable force field using reactant and product state topologies) has the unique property that it is able to take environmental effects into account leading to better convergence, a more faithful description of the transition state ensemble and therefore more accurate free energy profiles. However, E(gap) requires predefined topologies and is therefore inapplicable for multistate reactions, in which the barrier between the chemically equivalent topologies is comparable to the reaction activation barrier, because undesired "side reactions" occur. In this article, we introduce a new energy-based collective variable by generalizing the E(gap) reaction coordinate such that it becomes invariant to equivalent topologies and show that it yields more well behaved free energy profiles than simpler geometrical reaction coordinates.

Tests of an adaptive QM/MM calculation on free energy profiles of chemical reactions in solution.

We present reaction free energy calculations using the adaptive buffered force mixing quantum mechanics/molecular mechanics (bf-QM/MM) method. The bf-QM/MM method combines nonadaptive electrostatic embedding QM/MM calculations with extended and reduced QM regions to calculate accurate forces on all atoms, which can be used in free energy calculation methods that require only the forces and not the energy. We calculate the free energy profiles of two reactions in aqueous solution: the nucleophilic substitution reaction of methyl chloride with a chloride anion and the deprotonation reaction of the tyrosine side chain. We validate the bf-QM/MM method against a full QM simulation, and show that it correctly reproduces both geometrical properties and free energy profiles of the QM model, while the electrostatic embedding QM/MM method using a static QM region comprising only the solute is unable to do so. The bf-QM/MM method is not explicitly dependent on the details of the QM and MM methods, so long as it is possible to compute QM forces in a small region and MM forces in the rest of the system, as in a conventional QM/MM calculation. It is simple, with only a few parameters needed to control the QM calculation sizes, and allows (but does not require) a varying and adapting QM region which is necessary for simulating solutions.

Transient flow patterns and bubble slug lengths in parallel microchannels with oxygen gas bubbles produced by catalytic chemical reactions

Transient flow patterns and bubble slug lengths were investigated with oxygen gas (O-2) bubbles produced by catalytic chemical reactions using a high speed camera bonded with a microscope. The microreactor consists of an inlet liquid plenum, nine parallel rectangular microchannels followed by a micronozzle, using the MEMS fabrication technique. The etched surface was deposited by the thin platinum film, which is acted as the catalyst. Experiments were performed with the inlet mass concentration of the hydrogen peroxide from 50% to 90% and the pressure drop across the silicon chip from 2.5 to 20.0 kPa. The silicon chip is directly exposed in the environment thus the heat released via the catalytic chemical reactions is dissipated into the environment and the experiment was performed at the room temperature level. It is found that the two-phase flow with the catalytic chemical reactions display the cyclic behavior. A full cycle consists of a short fresh liquid refilling stage, a liquid decomposition stage followed by the bubble slug flow stage. At the beginning of the bubble slug flow stage, the liquid slug number reaches maximum, while at the end of the bubble slug flow stage the liquid slugs are quickly flushed out of the microchannels. Two or three large bubbles are observed in the inlet liquid plenum, affecting the two-phase distributions in microchannels. The bubble slug lengths, cycle periods as well as the mass flow rates are analyzed with different mass concentrations of hydrogen peroxide and pressure drops. The bubble slug length is helpful for the selection of the future microreactor length ensuring the complete hydrogen peroxide decomposition. Future studies on the temperature effect on the transient two-phase flow with chemical reactions are recommended.

State-to-state dynamics of elementary chemical reactions using Rydberg H-atom translational spectroscopy

In this review, a few examples of state-to-state dynamics studies of both unimolecular and bimolecular reactions using the H-atom Rydberg tagging TOF technique were presented. From the H2O photodissociation at 157 nm, a direction dissociation example is provided, while photodissociation of H2O at 121.6 has provided an excellent dynamical case of complicated, yet direct dissociation process through conical intersections. The studies of the O(D-1) + H-2 --> OH+H reaction has also been reviewed here. A prototype example of state-to-state dynamics of pure insertion chemical reaction is provided. Effect of the reagent rotational excitation and the isotope effect on the dynamics of this reaction have also been investigated. The detailed mechanism for abstraction channel in this reaction has also been closely studied. The experimental investigations of the simplest chemical reaction, the H-3 system, have also been described here. Through extensive collaborations between theory and experiment, the mechanism for forward scattering product at high collision energies for the H+HD reaction was clarified, which is attributed to a slow down mechanism on the top of a quantized barrier transition state. Oscillations in the product quantum state resolved different cross sections have also been observed in the H+D-2 reaction, and were attributed to the interference of adiabatic transition state pathways from detailed theoretical analysis. The results reviewed here clearly show the significant advances we have made in the studies of the state-to-state molecular reaction dynamics.

Design of silicone rubber according to requirements based on the multi-objective optimization of chemical reactions

The explicit expression between composition and mechanical properties of silicone rubber was derived from the physics of polymer elasticity, the implicit expression among material composition, reaction conditions and reaction efficiency was obtained from chemical thermodynamics and kinetics, and then an implicit multi-objective optimization model was constructed. Genetic algorithm was applied to optimize material composition and reaction conditions, and the finite element method of cross-linking reaction processes was used to solve multi-objective functions, on the basis of which a new optimization methodology of crosslinking reaction processes was established. Using this methodology, rubber materials can be designed according to pre-specified requirements.