Reaction path synthesis methodology for waste minimization

Being the core of whole process, a chemical process is a key step for reducing waste generation. Therefore, to organize a reasonable reaction path is very important for reducing waste emission. Because of the large amount of the feasible reaction path and other factors in a chemical reaction system, the opti-mizing for reaction path is difficult. Since the reaction path synthesis problem has presented, lots of re-searchers focused on it. At the beginning, only chem-ists took the research work,…     

A combined explicit-implicit method for high accuracy reaction path integration

We present the use of an optimal combined explicit-implicit method for following the reaction path to high accuracy. This is in contrast to most purely implicit reaction path integration algorithms, which are only efficient on stiff ordinary differential equations. The defining equation for the reaction path is considered to be stiff, however, we show here that the reaction path is not uniformly stiff and instead is only stiff near stationary points. The optimal algorithm developed in this work is a combination of explicit and implicit methods with a simple criterion to switch between the two. Using three different chemical reactions, we combine and compare three different integration methods: the implicit trapezoidal method, an explicit stabilized third order algorithm implemented in the code DUMKA3 and the traditional explicit fourth order Runge-Kutta method written in the code RKSUITE. The results for high accuracy show that when the implicit trapezoidal method is combined with either explicit method the number of energy and gradient calculations can potentially be reduced by almost a half compared with integrating either method alone. Finally, to explain the improvements of the combined method we expand on the concepts of stability and stiffness and relate them to the efficiency of integration methods.     

Determination of complex reaction mechanisms. Analysis of chemical, biological and genetic networks

We present several methods of determining, not guessing, complex chemical reaction mechanisms and their functions. One method is based on the theory of correlation functions of measured time series of concentrations of chemical species; another is on measurements of temporal responses of concentrations to various perturbations of arbitrary magnitude; a third deals with the analysis of oscillatory systems; a fourth is on the use of genetic algorithms to determine functions of chemical reaction networks. All methods are applicable to chemical, biochemical, and biological reaction systems and to genetic networks and systems biology. The methods depend on the design of appropriate experiments on the whole system and corresponding theories for interpretation that lead to information on the causal chemical connectivity of species, on reaction pathways, on reaction mechanisms, on control centers in the system, and on functions of the system. The first three methods require no assumption of a model or hypothesis, nor extensive calculations, unlike the interpretation of measurements made on a gene network at only one time.     

Examining the robustness of first-principles calculations for metal hydride reaction thermodynamics by detection of metastable reaction pathways

First principles calculations have played a useful role in screening mixtures of complex metal hydrides to find systems suitable for H(2) storage applications. Standard methods for this task efficiently identify the lowest energy reaction mechanisms among all possible reactions involving collections of materials for which DFT calculations have been performed. The resulting mechanism can potentially differ from physical reality due to inaccuracies in the DFT functionals used, or due to other approximations made in estimating reaction free energies. We introduce an efficient method to probe the robustness of DFT-based predictions that relies on identifying reactions that are metastable relative to the lowest energy reaction path predicted with DFT. An important conclusion of our calculations is that in many examples DFT cannot unambiguously predict a single reaction mechanism for a well defined metal hydride mixture because two or more mechanisms have reaction energies that differ by a small amount. Our approach is illustrated by analyzing a series of single step reactions identified in our recent work that examined reactions with a large database of solids [Kim et al., Phys. Chem. Chem. Phys. 2011, 13, 7218].     

An efficient molecular dynamics simulation method for calculating the diffusion-influenced reaction rates

We present a molecular dynamics (MD) simulation method for calculating the diffusion-influenced reaction rates in the limit of low reactant concentrations. To calculate the reaction rate coefficient, we use MD trajectories of a nonreactive equilibrium system that are initiated with a pair of reactant molecules in reactive configuration. Hence reaction systems involving complicated reactant molecules with geometrically restricted reactivities can be treated with comparable efficiency as the simple hard-sphere reaction system. Compared to the similar MD method proposed by Van Beijeren, Dong, and Bocquet [J. Chem. Phys. 114, 6265 (2001)], the present method has a couple of advantages. First, reactions involving more general sink functions can be treated. Second, more accurate results can be obtained when the reaction probability upon collision is less than unity. As an application, we investigate the effects of nondiffusive dynamics and hydrodynamic interaction of reactants on the reaction rate.     

Adapting the nudged elastic band method for determining minimum-energy paths of chemical reactions in enzymes

Optimization of reaction paths for enzymatic systems is a challenging problem because such systems have a very large number of degrees of freedom and many of these degrees are flexible. To meet this challenge, an efficient, robust and general approach is presented based on the well-known nudged elastic band reaction path optimization method with the following extensions: (1) soft spectator degrees of freedom are excluded from path definitions by using only inter-atomic distances corresponding to forming/breaking bonds in a reaction; (2) a general transformation of the distances is defined to treat multistep reactions without knowing the partitioning of steps in advance; (3) a multistage strategy, in which path optimizations are carried out for reference systems with gradually decreasing rigidity, is developed to maximize the opportunity of obtaining continuously changing environments along the path. We demonstrate the applicability of the approach using the acylation reaction of type A beta-lactamase as an example. The reaction mechanism investigated involves four elementary reaction steps, eight forming/breaking bonds. We obtained a continuous minimum energy path without any assumption on reaction coordinates, or on the possible sequence or the concertedness of chemical events. We expect our approach to have general applicability in the modeling of enzymatic reactions with quantum mechanical/molecular mechanical models.     

Steepest descent reaction path integration using a first-order predictor-corrector method

The theoretical treatment of chemical reactions inevitably includes the integration of reaction pathways. After reactant, transition structure, and product stationary points on the potential energy surface are located, steepest descent reaction path following provides a means for verifying reaction mechanisms. Accurately integrated paths are also needed when evaluating reaction rates using variational transition state theory or reaction path Hamiltonian models. In this work an Euler-based predictor-corrector integrator is presented and tested using one analytic model surface and five chemical reactions. The use of Hessian updating, as a means for reducing the overall computational cost of the reaction path calculation, is also discussed.     

Determination of initial reaction rates using wilkinson's relation

Uncertainty sometimes exists in determining initial reaction rates from experimental data. A method, originally proposed by Wilkinson [9] for estimating orders and rate constants for simple batch nth order reactions, has been generalized to complex kinetic systems. This method yields very accurate initial rates for all systems and extends the conversion range of experimental investigation of initial rates well beyond the “zero-order” region. Accurate initial rates are required in analytical methods used for screening alternate reaction mechanisms.     

Dynamics of the reaction glucose-catalase-glucose oxidase-hydrogen peroxide

Glucose-catalase-glucose oxidase-hydrogen peroxide reaction is one of the few known enzymatic systems studied in vitro in the field of nonlinear chemical dynamics. This reaction belongs to the family of oscillatory enzymatic reactions, which form a natural basis of oscillations in biological systems. A parametric study of dependence on mixing, temperature and initial concentrations of components in a batch stirred reactor was carried out. A newly proposed mathematical model of the reaction conforms to the obtained experimental data. Results of our experiments and simulations hint at further directions of research of non-linear dynamics in this reaction.     

Theoretical investigation of the gas-phase reaction of NiO+ with ethane

To explore the mechanisms for Ni-based oxide-catalyzed oxidative dehydrogenation (ODH) reactions, we investigate the reactions of C₂H₆ with NiO⁺ using density functional calculations. Two possible reaction pathways are identified, which lead to the formation of ethanol (path 1), ethylene and water (path 2). The proportion of products is discussed by Curtin-Hammett principle, and the result shows that path 2 is the main reaction channel and the water and ethylene are the main products. In order to get a deeper understanding of the titled reaction, numerous means of analysis methods including the atoms in molecules (AIM), electron localization function (ELF), natural bond orbital (NBO), and density of states (DOS) are used to study the properties of the chemical bonding evolution along the reaction pathways.

     

Cope reaction families: to be or not to be a biradical

The cyclization reactions of polyunsaturated systems such as enediynes, enyne-allenes, as well as many others, can be structurally related to the Cope reaction and grouped into two branches: 6pi (e.g., Cope, allenyl-Cope) and [2sigma + 4pi] systems (e.g., Bergman, Myers-Saito). After extensive computional (BCCD(T)/cc-pVDZ//UBLYP/6-31G) examination of a large set of Cope-related reactions, we derive the following simple rule: biradical intermediates are involved along the reaction path if they are stabilized by allylic resonance or aromaticity.     

Automatic integration of the reaction path using diagonally implicit Runge-Kutta methods

The diagonally implicit Runge-Kutta framework is shown to be a general form for constructing stable, efficient steepest descent reaction path integrators, of any order. With this framework tolerance driven, adaptive step-size methods can be constructed by embedding methods to obtain error estimates of each step without additional computational cost. There are many embedded and nonembedded, diagonally implicit Runge-Kutta methods available from the numerical analysis literature and these are reviewed for orders two, three, and four. New embedded methods are also developed which are tailored to the application of reaction path following. All integrators are summarized and compared for three systems: the Muller-Brown [Theor. Chem. Acta 53, 75 (1979)] potential and two gas phase chemical reactions. The results show that many of the methods are capable of integrating efficiently while reliably keeping the error bound within the desired tolerance. This allows the reaction path to be determined through automatic integration by only specifying the desired accuracy and transition state.     

The Preparation of β-Cycloalkyl-L-Aspartate and γ-Cycloalkyl-L-Glutamate by Enzymatic Hydrolyses

The simple method to prepare the β-cycloalkyl aspartate and γ-cycloalkyl glutamate by enzymatic reactions has been developed. Compared with conventional chemical methods, the enzymatic method is more facile.     

Multistructural microiteration technique for geometry optimization and reaction path calculation in large systems

We propose a multistructural microiteration (MSM) method for geometry optimization and reaction path calculation in large systems. MSM is a simple extension of the geometrical microiteration technique. In conventional microiteration, the structure of the non‐reaction‐center (surrounding) part is optimized by fixing atoms in the reaction‐center part before displacements of the reaction‐center atoms. In this method, the surrounding part is described as the weighted sum of multiple surrounding structures that are independently optimized. Then, geometric displacements of the reaction‐center atoms are performed in the mean field generated by the weighted sum of the surrounding parts. MSM was combined with the QM/MM‐ONIOM method and applied to chemical reactions in aqueous solution or enzyme. In all three cases, MSM gave lower reaction energy profiles than the QM/MM‐ONIOM‐microiteration method over the entire reaction paths with comparable computational costs. © 2017 Wiley Periodicals, Inc.     

Efficiency analysis of reaction rate calculation methods using analytical models I: The two-dimensional sharp barrier

We analyze the efficiency of different methods for the calculation of reaction rates in the case of a simple two-dimensional analytical benchmark system. Two classes of methods are considered: the first is based on the free energy calculation along a reaction coordinate and the calculation of the transmission coefficient, the second on the sampling of dynamical pathways. We give scaling rules for how this efficiency depends on barrier height and width, and we hand out simple optimization rules for the method-specific parameters. We show that the path sampling methods, using the transition interface sampling technique, become exceedingly more efficient than the others when the reaction coordinate is not the optimal one.     

New Aspects of Protein‐film Voltammetry of Redox Enzymes Coupled to Follow‐up Reversible Chemical Reaction in Square‐wave Voltammetry

Protein‐film square‐wave voltammetry of uniformly adsorbed molecules of redox lipophilic enzymes is applied to study their electrochemical properties, when a reversible follow‐up chemical reaction is coupled to the electrochemically generated product of enzyme's electrode reaction. Theoretical consideration of this so‐called “surface ECrev mechanism” under conditions of square‐wave voltammetry has revealed several new aspects, especially by enzymatic electrode reactions featuring fast electron transfer. We show that the rate of chemical removal/resupply of electrochemically generated Red(ads) enzymatic species, shows quite specific features to all current components of calculated square‐wave voltammograms and affects the electrode kinetics. The effects observed are specific for this particular redox mechanism (surface ECrev mechanism), and they got more pronounced at high electrode kinetics of enzymatic reaction. The features of phenomena of “split net‐SWV peak” and “quasireversible maximum”, which are typical for surface redox reactions studied in square‐wave voltammetry, are strongly affected by kinetics and thermodynamics of follow‐up chemical reaction. While we present plenty of relevant voltammetric situations useful for recognizing this particular mechanism in square‐wave voltammetry, we also propose a new approach to get access to kinetics and thermodynamics of follow‐up chemical reaction. Most of the results in this work throw new insight into the features of protein‐film systems that are coupled with chemical reactions.     

First-principles molecular dynamics simulations of condensed-phase V-type nerve agent reaction pathways and energy barriers

Computational studies of condensed-phase chemical reactions are challenging in part because of complexities in understanding the effects of the solvent environment on the reacting chemical species. Such studies are further complicated due to the demanding computational resources required to implement high-level ab initio quantum chemical methods when considering the solvent explicitly. Here, we use first-principles molecular dynamics simulations to examine condensed-phase decontamination reactions of V-type nerve agents in an explicit aqueous solvent. Our results include a detailed study of hydrolysis, base-hydrolysis, and nucleophilic oxidation of both VX and R-VX, as well as their protonated counterparts (i.e., VXH(+) and R-VXH(+)). The decontamination mechanisms and chemical reaction energy barriers, as determined from our simulations, are found to be in good agreement with experiment. The results demonstrate the applicability of using such simulations to assist in understanding new decontamination technologies or other applications that require computational screening of condensed-phase chemical reaction mechanisms.     

A theoretical insight into the reaction mechanism of photochemical transposition from pyrazole to imidazole

The mechanisms of the photochemical isomerization reactions were investigated by using a model system of 1,3,5-trimethylpyrazole ( 1) with the CASSCF (eight-electron/six-orbital active space) and MP2-CAS methods and the 6-311G(d) basis set. Three reaction pathways were examined in the present work. They are denoted as the ring-contraction-ring-expansion path (path I), the internal-cyclization-isomerization path (path II), and the conical-intersection path (path III). Our model investigations suggest that the preferred reaction route for the pyrazoles is as follows: reactant --> Franck-Condon region --> conical intersection --> photoproduct. In particular, the conical-intersection mechanism (path III) found in this work gives a better explanation than the previously proposed two other mechanisms (paths I and II). The theoretical findings also indicate that path III-1 should be favored over path III-2 from a kinetic point of view. This suggests that the quantum yield of 1,2,4-trimethylimidazole ( 2) should be greater than that of 1,2,5-trimethylimidazole ( 3), which supports the available experimental observations. Additionally, we propose a simple p-pi orbital topology model, which can be used as a diagnostic tool to predict the location of the conical intersections, as well as the geometries of the phototransposition products of various heterocycles.     

Reaction path potential for complex systems derived from combined ab initio quantum mechanical and molecular mechanical calculations

Combined ab initio quantum mechanical and molecular mechanical calculations have been widely used for modeling chemical reactions in complex systems such as enzymes, with most applications being based on the determination of a minimum energy path connecting the reactant through the transition state to the product in the enzyme environment. However, statistical mechanics sampling and reaction dynamics calculations with a combined ab initio quantum mechanical (QM) and molecular mechanical (MM) potential are still not feasible because of the computational costs associated mainly with the ab initio quantum mechanical calculations for the QM subsystem. To address this issue, a reaction path potential energy surface is developed here for statistical mechanics and dynamics simulation of chemical reactions in enzymes and other complex systems. The reaction path potential follows the ideas from the reaction path Hamiltonian of Miller, Handy and Adams for gas phase chemical reactions but is designed specifically for large systems that are described with combined ab initio quantum mechanical and molecular mechanical methods. The reaction path potential is an analytical energy expression of the combined quantum mechanical and molecular mechanical potential energy along the minimum energy path. An expansion around the minimum energy path is made in both the nuclear and the electronic degrees of freedom for the QM subsystem internal energy, while the energy of the subsystem described with MM remains unchanged from that in the combined quantum mechanical and molecular mechanical expression and the electrostatic interaction between the QM and MM subsystems is described as the interaction of the MM charges with the QM charges. The QM charges are polarizable in response to the changes in both the MM and the QM degrees of freedom through a new response kernel developed in the present work. The input data for constructing the reaction path potential are energies, vibrational frequencies, and electron density response properties of the QM subsystem along the minimum energy path, all of which can be obtained from the combined quantum mechanical and molecular mechanical calculations. Once constructed, it costs much less for its evaluation. Thus, the reaction path potential provides a potential energy surface for rigorous statistical mechanics and reaction dynamics calculations of complex systems. As an example, the method is applied to the statistical mechanical calculations for the potential of mean force of the chemical reaction in triosephosphate isomerase.     

Understanding the physics and chemistry of reaction mechanisms from atomic contributions: a reaction force perspective

Studying chemical reactions involves the knowledge of the reaction mechanism. Despite activation barriers describing the kinetics or reaction energies reflecting thermodynamic aspects, identifying the underlying physics and chemistry along the reaction path contributes essentially to the overall understanding of reaction mechanisms, especially for catalysis. In the past years the reaction force has evolved as a valuable tool to discern between structural changes and electrons' rearrangement in chemical reactions. It provides a framework to analyze chemical reactions and additionally a rational partition of activation and reaction energies. Here, we propose to separate these energies further in atomic contributions, which will shed new insights in the underlying reaction mechanism. As first case studies we analyze two intramolecular proton transfer reactions. Despite the atom based separation of activation barriers and reaction energies, we also assign the participation of each atom in structural changes or electrons' rearrangement along the intrinsic reaction coordinate. These participations allow us to identify the role of each atom in the two reactions and therfore the underlying chemistry. The knowledge of the reaction chemistry immediately leads us to suggest replacements with other atom types that would facilitate certain processes in the reaction. The characterization of the contribution of each atom to the reaction energetics, additionally, identifies the reactive center of a molecular system that unites the main atoms contributing to the potential energy change along the reaction path.