TRANSITIVITY CODE

Description

Recent advances in phenomenological descriptions of the kinetics of rate processes (Aquilanti et al., 2010, 2017, 2018) motivated this code based on detailed formulations given in previous works. Here, we document the Transitivity Code, written in Python, a free open-source code compatible with Windows and Linux platforms. Using the output from Gaussian as input files, the internal energy, enthalpy, Gibbs-free energy and partition functions for molecular entities involved in a chemical process can be catalogued. For unimolecular and bimolecular processes, the barrier height and the reaction rate constant can be calculated by traditional Transition-State Theory using a set of one-dimensional tunneling corrections: Bell35, Bell8, Skodje-Truhlar and in particular the d-model. To account for the solvent effect on reaction rate constant, implementation is given of the Kramers and Collins-Kimball formulations, which provide coefficients of friction and viscosity, the transmission coefficients, the diffusion rate constant, the diffusion coefficients and the overall reaction rate constants. Procedures are made available for the phenomenology of the temperature dependence of reaction rate constants beyond that of Arrhenius, specifically according to Aquilanti-Mundim (AM), Vogel–Fulcher–Tammann (VFT), Nakamura-Takayanagi-Sato (NTS) and Aquilanti-Sanchez-Coutinho-Carvalho (ASCC) formulas: use is made of the Generalized Simulated Annealing stochastic optimization method. An input file generator is provided to run various molecular dynamics approaches (Car-Parrinello, Born-Oppenheimer, Metadynamics, Trajectory Surface Hopping and Path-Integral) in CPMD code. The following examples are worked out and made available for testing: i) estimation of the reaction rate constants for the OH + HCl => H2O + Cl gas-phase reaction; ii) estimation of the reaction rate-constants for NH3 + OH => H2O + NH2 reaction including the solvent effect; iii) explicit fitting of the temperature dependence of the reaction rate constants for a series of reactions exhibiting sub-, super- and anti-Arrhenius behavior and iv) CPMD input files generator for benzoic acid. Novelty of this code is its general scope and particular exploit of d-formulations (Aquilanti-Mundim, ASCC formulas and the d-TST model), developed by our group to cope with non-Arrhenius behavior at low temperatures, a topic at focus of recent intense investigations.

Examples

The following examples are available for testing:

I. Gas-phase reaction: OH + HCl -> H2O + Cl;

II. Solvent effect: NH2 + OH -> H2O + NH2;

III. Fitting the temperature dependence of the reaction rate constant to: (A) OH + H2 -> H2O + H (sub-Arrhenius / moderate), b) intramolecular proton-transfer in Benzolate (sub-Arrhenius / deep), c) hydrogen-transfer in enzymes catalysis (super- Arrhenius) and d) OH + HBr -> H2O + Br (anti-Arrhenius);

IV. CPMD generator input files for benzoic acid

Documentation

a) Manual - PDF

b) Preparation and Installation video - VIDEO

c) Examples - OUTPUT

Developers

Hugo Machado
Flávio Sanches-Neto
Nayara Coutinho
Kleber Mundim
Vincenzo Aquilanti
Valter Carvalho-Silva

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