Chemical transformations involving the diffusion of reactants and subsequent chemical fixation steps are generally termed "diffusion-influenced reactions" (DIR). Virtually all biochemical processes in living media can be counted among them, together with those occurring in an ever-growing number of emerging nano-technologies. The role of the environment's geometry (obstacles, compartmentalization) and distributed reactivity (competitive reactants, traps) is key in modulating the rate constants of DIRs, and is therefore a prime design parameter. Yet, it is a formidable challenge to build a comprehensive theory that is able to describe the environment's "reactive geometry". Here we show that such a theory can be built by unfolding this many-body problem through addition theorems for special functions. Our method is powerful and general and allows one to study a given DIR reaction occurring in arbitrary "reactive landscapes", made of multiple spherical boundaries of given size and reactivity. Importantly, ready-to-use analytical formulas can be derived easily in most cases.
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http://dx.doi.org/10.1039/c6cp01147k | DOI Listing |
J Chem Phys
August 2024
Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 4 Kosygina St., 119991 Moscow, Russian Federation.
Motivated by the various applications of the trapping diffusion-influenced reaction theory in physics, chemistry, and biology, this paper deals with irreducible Cartesian tensor (ICT) technique within the scope of the generalized method of separation of variables (GMSV). We provide a survey from the basic concepts of the theory and highlight the distinctive features of our approach in contrast to similar techniques documented in the literature. The solution to the stationary diffusion equation under appropriate boundary conditions is represented as a series in terms of ICT.
View Article and Find Full Text PDFJ Chem Phys
October 2023
Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan.
The returning probability (RP) theory, a rigorous diffusion-influenced reaction theory, enables us to analyze the binding process systematically in terms of thermodynamics and kinetics using molecular dynamics (MD) simulations. Recently, the theory was extended to atomistically describe binding processes by adopting the host-guest interaction energy as the reaction coordinate. The binding rate constants can be estimated by computing the thermodynamic and kinetic properties of the reactive state existing in the binding processes.
View Article and Find Full Text PDFBiopolymers
January 2024
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, 20892, USA.
The simplest way to account for the influence of diffusion on the kinetics of multisite phosphorylation is to modify the rate constants in the conventional rate equations of chemical kinetics. We have previously shown that this is not enough and new transitions between the reactants must also be introduced. Here we extend our results by considering enzymes that are inactive after modifying the substrate and need time to become active again.
View Article and Find Full Text PDFLangmuir
June 2021
Applied Theoretical Physics-Computational Physics, Physikalisches Institut, Albert-Ludwigs-Universität Freiburg, Hermann-Herder Strasse 3, D-79104 Freiburg, Germany.
Electrostatic reaction inhibition in heterogeneous catalysis emerges if charged reactants and products with similar charges are adsorbed on the catalyst and thus repel the approaching reactants. In this work, we study the effects of electrostatic inhibition on the reaction rate of unimolecular reactions catalyzed on the surface of a spherical model nanoparticle using particle-based reaction-diffusion simulations. Moreover, we derive closed rate equations based on an approximate Debye-Smoluchowski rate theory, valid for diffusion-controlled reactions, and a modified Langmuir adsorption isotherm, relevant for reaction-controlled reactions, to account for electrostatic inhibition in the Debye-Hückel limit.
View Article and Find Full Text PDFJ Phys Chem B
March 2021
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States.
Enzymatic cascade reactions, where a substrate is converted into a product in several steps, play a critical role in many biological systems. The enzymes in such reactions are often clustered inside intracellular compartments. To understand the effect of localization, we develop a theory for cascade reactions converting substrates into intermediates and then into products when the enzymes are localized in clusters.
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