On the study of nonlinear dynamics of complex chemical reaction systems

When driven far from equilibrium,nonlinear chemical reactions often show a variety of self-organization behavior,including chemical oscillations,waves,chaos and patterns[1].Recently,the study of such nonlinear phenomena in‘complex’systems,such as the li…     

Propagation of Oscillating Chemical Signals through Reaction Networks

Akin to electronic systems that can tune to and process signals of select frequencies, systems/networks of chemical reactions also “propagate” time‐varying concentration inputs in a frequency‐dependent manner. Whereas signals of low frequencies are transmitted, higher frequency inputs are dampened and converted into steady‐concentration outputs. Such behavior is observed in both idealized reaction chains as well as realistic signaling cascades, in the latter case explaining the experimentally observed responses of such cascades to input calcium oscillations. These and other results are supported by numerical simulations within the freely available Kinetix web application we developed to study chemical systems of arbitrary architectures, reaction kinetics, and boundary conditions.     

Monotone Chemical Reaction Networks

We analyze certain chemical reaction networks and show that every solution converges to some steady state. The reaction kinetics are assumed to be monotone but otherwise arbitrary. When diffusion effects are taken into account, the conclusions remain unchanged. The main tools used in our analysis come from the theory of monotone dynamical systems. We review some of the features of this theory and provide a self-contained proof of a particular attractivity result which is used in proving our main result.     

Probing the bent bonds in cyclopropane systems for gas storage and separation process: A computational study

The hydrogen, carbon dioxide, and carbon monoxide gas adsorption and storage capacity of lithium-decorated cyclopropane ring systems were examined with quantum chemical calculations at density functional theory, DFT M06-2X functional using 6-31G(d) and cc-pVDZ basis sets. To examine the reliability of M06-2X DFT functional, a few representative systems are also examined with complete basis set CBS-QB3 method and CCSD-aug-cc-pVTZ level of theory. The cyclopropane systems can bind to one Li⁺ ion; however, the corresponding the methylated systems can bind with two Li⁺ ions. The cyclopropane systems can adsorb six hydrogen molecules with an average binding energy of 3.8 kcal/mol. The binding free energy (ΔG) values suggest that the hydrogen adsorption process is feasible at 273.15 K. The calculation of desorption energies indicates the recyclable property of gas adsorbed complexes. The same number of CO₂ and CO gas molecules can also be adsorbed with an average binding energy of −14.4 kcal/mol and −10.7 kcal/mol, respectively. The carbon dioxide showed ~3–4 kcal/mol better binding energy as compared to carbon monoxide and hence such designed systems can function as a potential candidate for the separation of these flue gas molecules. The nature of interactions in complexes was examined with atoms in molecules analysis revealed the electrostatic nature for the interaction of Li⁺ ion with cyclopropane rings. The chemical hardness and electrophilicity calculations showed that the gas adsorbed complexes are rigid and therefore robust as gas storage materials.     

化学结构正规编码及其信息处理功能

自从计算机在化学领域中应用以来,化学结构的正规编码已广泛用来作为一种化学文献的信息索引,它还在开发化学智能系统中发挥着重要作用。正规编码生成是以化学结构图的拓扑性质为基础的。本文首先概述编码的基本原理及其生成的方法,随后分析这种编码在当今文献数据库、化学反应数据库、分子设计以及合成反应路线规划等化学信息系统中的功能。     

Organocatalytic Control over a Fuel-Driven Transient-Esterification Network**

Signal transduction in living systems is the conversion of information into a chemical change, and is the principal process by which cells communicate. In nature, these functions are encoded in non-equilibrium (bio)chemical reaction networks (CRNs) controlled by enzymes. However, man-made catalytically controlled networks are rare. We incorporated catalysis into an artificial fuel-driven out-of-equilibrium CRN, where the forward (ester formation) and backward (ester hydrolysis) reactions are controlled by varying the ratio of two organocatalysts: pyridine and imidazole. This catalytic regulation enables full control over ester yield and lifetime. This fuel-driven strategy was expanded to a responsive polymer system, where transient polymer conformation and aggregation are controlled through fuel and catalyst levels. Altogether, we show that organocatalysis can be used to control a man-made fuel-driven system and induce a change in a macromolecular superstructure, as in natural non-equilibrium systems.     

Structural analysis of certain linear operators representing chemical network systems via the existence and uniqueness theorems of spectral resolution. III

By extending the methodology given in Parts I and II of this series of articles, certain dynamical systems of chemical kinetic equations are analyzed in the setting of the Banach algebra B(ℬ︁) of all bounded operators acting on a Banach space ℬ︁. In this article, we proceed from the general setting of B(ℬ︁), which played a central role in Part II, toward its specific application to the dynamical systems. In our analysis, crucial initial steps are taken by (i) equipping the abstract space ℬ︁ with the “positive quadrant,” which we denote by Γ(ℝ⁺ⁿ), and by (ii) investigating the asymptotic behavior of the solution χ_ϵ(t) of the initial-value problem is suitably specified for our application purposes. The main theorem and its two specialized versions, together with the notions of Γ-semipositive operators and semipositive matrices presented here, serve as fundamental tools for the analysis of a class of dynamical systems of chemical kinetic equations whose examples were illustratively treated in the previous parts of this series of articles. The techniques developed here for an asymptotic analysis of chemical kinetic dynamical systems will be linked and unified with those for the asymptotic analysis of quantum mechanical systems in a forthcoming part of this series of articles. © 1997 John Wiley & Sons, Inc. Int J Quant Chem 63: 149–163, 1997     

Retention in field-flow fractionation with secondary chemical equilibria

Summary The application range of field-flow fractionation (FFF) can be extended to low molecular weight solutes, as demonstrated a few years ago by Berthod et al., by taking profit of secondary chemical equilibria (SCE) occurring between the bulk carrier and a retained carrier component. The theory of solute retention in this SCE-FFF method is developed for any value of the solute distribution coefficient and of the retention ratio of the retained carrier component, provided that the Brownian mode of retention applies for this component and that the flow velocity profile is parabolic. This removes some of the limitations of the model previously developed by Berthod and Armstrong and sheds light on the potentialities of the SCE-FFF method for physico-chemical studies about secondary chemical equilibria in colloidal systems. Remaining assumptions in the model are discussed.Dedicated to Professor Leslie S. Ettre on the occasion of his 70th birthday.     

The Coordinate Reaction Model: An Obstacle to Interpreting the Emergence of Chemical Complexity

The way chemical transformations are described by models based on microscopic reversibility does not take into account the irreversibility of natural processes, and therefore, in complex chemical networks working in open systems, misunderstandings may arise about the origin and causes of the stability of non-equilibrium stationary states, and general constraints on evolution in systems that are far from equilibrium. In order to be correctly simulated and understood, the chemical behavior of complex systems requires time-dependent models, otherwise the irreversibility of natural phenomena is overlooked. Micro reversible models based on the reaction-coordinate model are time invariant and are therefore unable to explain the evolution of open dissipative systems. The important points necessary for improving the modeling and simulations of complex chemical systems are: a) understanding the physical potential related to the entropy production rate, which is in general an inexact differential of a state function, and b) the interpretation and application of the so-called general evolution criterion (GEC), which is the general thermodynamic constraint for the evolution of dissipative chemical systems.     

DNA Reaction–Diffusion Attractor Patterns

Living systems can form and recover complex chemical patterns with precisely sized features in the ranges of tens or hundreds of microns. We show how designed reaction–diffusion processes can likewise produce precise patterns, termed attractor patterns, that reform their precise shape after being perturbed. We use oligonucleotide reaction networks, photolithography, and microfluidic delivery to form precisely controlled attractor patterns and study the responses of these patterns to different localized perturbations. Linear and “hill”‐shaped patterns formed and stabilized into shapes and at time scales consistent with reaction–diffusion models. When patterns were perturbed in particular locations with UV light, they reliably reformed their steady‐state profiles. Recovery also occurred after repeated perturbations. By designing the far‐from‐equilibrium dynamics of a chemical system, this study shows how it is possible to design spatial patterns of molecules that are sustained and regenerated by continually evolving towards a specific steady state configuration.     

Time dependence of the NMR line shape for systems with chemical exchange in a zero saturation limit

An expression has been derived for the time dependence of the NMR line shape for systems with many-site chemical exchange in the absence of spin-spin coupling, in a zero saturation limit. The dynamics of variation of the NMR line shape with time is considered in detail for the case of two-site chemical exchange. Mathematica programs have been designed for numerical simulation of the NMR spectra of chemical exchange systems. The analytical expressions obtained are useful for NMR line shape simulations for systems with photoinduced chemical exchange.     

Structural importance of secondary interactions in molecules: origin of unconventional conformations of phosphine-borane adducts

The series of phosphine-borane adducts, Ph2(H3C--C[triple chemical bond]C)P--B(C6F5)3 (8 c), Ph(H3C--C[triple chemical bond]C)2P--B(C6F5)3 (8 b) and (H3C--C[triple chemical bond]C)3P--B(C6F5)3 (8 a), was prepared. The X-ray crystal structure analyses revealed close to eclipsed conformations for all members of this series with average dihedral angles theta(C-P-B-C) of 8.1 degrees (8 c), 12.3 degrees (8 b) and 20.3 degrees (8 a). Quantum chemical analysis of these compounds revealed the importance of a subtle interplay between competing attractive and repulsive secondary interactions, causing the surprising eclipsed conformational preference for systems of this degree of complexity. Some cyclic phosphine-borane adducts were studied for comparison.     

Groups of Organic Molecules That Operate Collectively

A “chemical system” is defined as an assemblage of molecules that collectively does something interesting or useful. The key word here is “collectively”, a word that implies an interdependency and a group behavior that can be quite different from that of individual molecules. Batteries, computer chips, concrete, mayonnaise, shampoo, paint, liquid crystal displays, composites, and viruses are all examples of commonly encountered systems. A host–guest or “supramolecular” complex, on the other hand, would not be considered a system (as defined here), because only two species are involved. A chemical system is multimolecular, a collection of molecules interlocked in a tangle of dependencies. The review delves into a variety of chemical systems investigated by the author, including micelles, water pools, films, vesicles, and polymers. All of them can be categorized as “self-assembling” or “self-organizing” in the sense that defined structures arise spontaneously owing to noncovalent forces among the component molecules. Such chemical systems are useful for many purposes, including decontamination of environmentally dangerous substances, drug delivery, and separation of organic compounds.     

介观化学体系中的动力学尺度效应

以生命和表面催化体系为对象,研究了介观化学体系中内涨落对体系非线性动力学行为的调控作用。内涨落可以诱导随机振荡,其强度在体系处于最佳尺度时会出现一个甚至多个极大值,并且在耦合体系中会得到进一步增强,表现为尺度共振效应、尺度选择效应和双重尺度效应,揭示了介观化学体系中尺度效应的新机制。     

介观化学体系中的动力学尺度效应

以生命和表面催化体系为对象,研究了介观化学体系中内涨落对体系非线性动力学行为的调控作用。内涨落可以诱导随机振荡,其强度在体系处于最佳尺度时会出现一个甚至多个极大值,并且在耦合体系中会得到进一步增强,表现为尺度共振效应、尺度选择效应和双重尺度效应,揭示了介观化学体系中尺度效应的新机制。     

Supersaturation-Based Drug Delivery Systems: Strategy for Bioavailability Enhancement of Poorly Water-Soluble Drugs

At present, the majority of APIs synthesized today remain challenging tasks for formulation development. Many technologies are being utilized or explored for enhancing solubility, such as chemical modification, novel drug delivery systems (microemulsions, nanoparticles, liposomes, etc.), salt formation, and many more. One promising avenue attaining attention presently is supersaturated drug delivery systems. When exposed to gastrointestinal fluids, drug concentration exceeds equilibrium solubility and a supersaturation state is maintained long enough to be absorbed, enhancing bioavailability. In this review, the latest developments in supersaturated drug delivery systems are addressed in depth.     

Selenium and Selenocysteine in Protein Chemistry

Selenocysteine, the selenium‐containing analogue of cysteine, is the twenty‐first proteinogenic amino acid. Since its discovery almost fifty years ago, it has been exploited in unnatural systems even more often than in natural systems. Selenocysteine chemistry has attracted the attention of many chemists in the field of chemical biology owing to its high reactivity and resulting potential for various applications such as chemical modification, chemical protein (semi)synthesis, and protein folding, to name a few. In this Minireview, we will focus on the chemistry of selenium and selenocysteine and their utility in protein chemistry.     

Theoretical methods in thermodynamics of condensed phases

Theoretical possibilities of determining energetic and thermodynamic characteristics of chemical entities in gaseous and condensed (solid and liquid) phases are briefly reviewed. The considerations include quantum chemistry methods which enable evaluation of energetic quantities and statistical thermodynamics dependencies necessary for determining other thermodynamic characteristics. The possible applications of these methods are also discussed in brief.     

On the Nonlinear Dynamic State Reconstruction Problem for Chemical/Biochemical Reaction Systems in the Presence of Model Uncertainty

A new approach to the unmeasurable state reconstruction problem for nonlinear chemical reaction systems in the presence of model uncertainty is proposed. In particular, a new robust nonlinear state estimation method is developed that explicitly uses all the available useful information associated with: (i) a dynamic model inevitably characterized by uncertainty, and (ii) a set of sensor measurements in order to accurately reconstruct other key quantities/variables that cannot be measured on-line due to physical and/or technical limitations. The problem of interest is conveniently formulated and addressed within the context of singular partial differential equations (PDE) theory, leading to a nonlinear state estimator that possesses a state-dependent gain computed through the solution of a system of first-order singular PDEs. A set of necessary and sufficient conditions is presented that ensure the existence and uniqueness of a locally analytic solution to the aforementioned system of singular PDEs, and a series solution method that can be easily implemented via a MAPLE code is developed. Under these conditions, the convergence of the estimation error or the mismatch between the actual unmeasurable states and their estimates is analyzed and characterized in the presence of model uncertainty. Finally, the performance of the proposed nonlinear etimator and its convergence properties are evaluated in an illustrative biochemical reaction system that exhibits nonlinear behavior coupled with parametric uncertainty, and the estimation objective is to accurately reconstruct the unmeasurable substrate concentration using the available cell mass concentration measurements and the model of the system under consideration.