Abstract
The Transitivity function, defined in terms of the reciprocal of the apparent activation energy, measures the propensity for a reaction to proceed and can provide a tool for implementing phenomenological kinetic models. Applications to systems which deviate from the Arrhenius law at low temperature encouraged the development of a user-friendly graphical interface for estimating the kinetic and thermodynamic parameters of physical and chemical processes. Here, we document the Transitivity code, written in Python, a free open-source code compatible with Windows, Linux and macOS platforms. Procedures are made available to evaluate the phenomenology of the temperature dependence of rate constants for processes from the Arrhenius and Transitivity plots. Reaction rate constants can be calculated by the traditional Transition-State Theory using a set of one-dimensional tunneling corrections (Bell (1935), Bell (1958), Skodje and Truhlar and, in particular, the deformed (-TST) approach). To account for the solvent effect on reaction rate constant, implementation is given of the Kramers and of Collins–Kimball formulations. An input file generator is provided to run various molecular dynamics approaches in CPMD code. Examples are worked out and made available for testing. The novelty of this code is its general scope and particular exploit of -formulations to cope with non-Arrhenius behavior at low temperatures, a topic which is the focus of recent intense investigations. We expect that this code serves as a quick and practical tool for data documentation from electronic structure calculations: It presents a very intuitive graphical interface which we believe to provide an excellent working tool for researchers and as courseware to teach statistical thermodynamics, thermochemistry, kinetics, and related areas.
Highlights
Recent applications of chemical kinetics to a variety of complex systems involves the accurate dealing of properties to be described by techniques, which treat a series of processes beyond elementary chemical quantum dynamics or even approximate classical and semiclassical approaches
The current status of the phenomenology is classified emphasizing case studies, (i) super-Arrhenius kinetics, convex curvature in the Arrhenius plot, where transport phenomena brakes the processes as temperature decreases; (ii) sub-Arrhenius kinetics, concave curvature in the Arrhenius plot, where quantum mechanical tunneling propitiates low temperature reactivity; (iii) anti-Arrhenius kinetics, negative apparent activation energy, where processes are limited by stereodynamic requirements
It offers the possibility of estimating phenomenological parameters from Arrhenius and Transitivity plots using a stochastic optimization method, Generalized Simulated Annealing (GSA) [55], with several options: Arrhenius, Aquilanti–Mundim (AM) [25], Vogel–Fulcher–Tammann (VFT) [22], Nakamura–Takayanagi–Sato (NTS) [24,56] and Aquilanti–Sanchez–Coutinho–Carvalho (ASCC) [26] formulas
Summary
Recent applications of chemical kinetics to a variety of complex systems involves the accurate dealing of properties to be described by techniques, which treat a series of processes beyond elementary chemical quantum dynamics or even approximate classical and semiclassical approaches. We describe a new code with a user-friendly graphical interface able to perform various procedures for computing kinetic and related parameters in chemical transformations and transport phenomena: The code is referred to as “Transitivity” (see Figure 1), a concept related to the function defined in Equation (2); written in Python, it is a free open-source code compatible with Windows, Linux, and MacOS platforms It offers the possibility of estimating phenomenological parameters from Arrhenius and Transitivity plots using a stochastic optimization method, Generalized Simulated Annealing (GSA) [55], with several options: Arrhenius, Aquilanti–Mundim (AM) [25], Vogel–Fulcher–Tammann (VFT) [22], Nakamura–Takayanagi–Sato (NTS) [24,56] and Aquilanti–Sanchez–Coutinho–Carvalho (ASCC) [26] formulas.
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