Pilgrim is a program written in Python and designed to use direct dynamics in the calculation of thermal rate constants of chemical reactions by the variational transition state theory (VTST), based on electronic structure calculations for the potential energy surface. Pilgrim can also simulate reaction mechanisms using kinetic Monte Carlo (KMC). For reaction processes with many elementary steps, the rate constant of each of these steps can be calculated by means of conventional transition state theory (TST) or by using VTST. In the current version, Pilgrim can evaluate thermal rates using the canonical version of reaction-path VTST, which requires the calculation of the minimum energy path (MEP) associated with each elementary step or transition structure. Multi-dimensional quantum effects can be incorporated through the small-curvature tunneling (SCT) approximation. These methodologies are available both for reactions involving a single structure of the reactants and the transition state and also for reactions involving flexible molecules with multiple conformations of the reactant and/or of the transition state. For systems with many conformers, the program can evaluate each of the elementary reaction rate constants by multipath canonical VTST or multi-structural VTST. Moreover, the reactant can be unimolecular or bimolecular. Torsional anharmonicity can be incorporated through either the MSTor or the Q2DTor programs. Dual-level calculations are also available in Pilgrim: automatic high-level single-point energies can be used to correct the energy of reactants, transition states, products, and MEP points using the interpolated single-point energies (ISPE) algorithm. When the rate constants of all the chemical processes of interest are known, by means of their calculation using Pilgrim or alternatively through analytical fits to the rate constants as functions of temperature, it is possible to simulate a multistep mechanism under specified laboratory conditions using KMC. This algorithm allows performing a kinetic simulation to monitor the evolution of each chemical species with time and obtain the product yields. Program summary: Program Title: Pilgrim CPC Library link to program files: http://dx.doi.org/10.17632/24cj4dwxvg.1 Developer's repository link: https://github.com/cathedralpkg/pilgrim/releases; https://comp.chem.umn.edu/pilgrim; https://conservancy.umn.edu/handle/11299/166578 Licensing provisions: MIT Programming language: Python 3 Nature of problem: Calculation of thermal rate constants for bimolecular and unimolecular chemical reactions and simulation of reaction mechanisms Solution method: The program uses variational transition state theory to calculate thermal rate constants and kinetic Monte Carlo to simulate reaction mechanisms. Restrictions and unusual features: The program cannot treat reactions without saddle points. Unimolecular reactions are calculated only in the high-pressure limit. Direct dynamics calculations with Pilgrim require an electronic structure package to be supplied by the user; currently, Pilgrim supports the Gaussian [Frisch et al. (2003), Frisch et al. (2016a), Frisch et al. (2016b)] and Orca [Neese (2011)] electronic structure packages. Pilgrim has an especially powerful suite of options for handling torsional anharmonicity and multistructural effects.
Bibliographical noteFunding Information:
The authors thank ?Centro de Supercomputaci?n de Galicia (CESGA)? for the use of their computational facilities. Financial support from the Conseller?a de Cultura, Educaci?n e Ordenaci?n Universitaria, Spain (Axuda para Consolidaci?n e Estructuraci?n de unidades de investigaci?n competitivas do Sistema Universitario de Galicia, Xunta de Galicia ED431C 2017/17 & Centro singular de investigaci?n de Galicia acreditaci?n 2019?2022, Spain, ED431G 2019/03) and the European Regional Development Fund (ERDF) is gratefully acknowledged. D. F-C. thanks Xunta de Galicia, Spain for financial support through a postdoctoral grant. This work was supported in part by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences under Award DE-SC0015997.
The authors thank “Centro de Supercomputación de Galicia (CESGA)” for the use of their computational facilities. Financial support from the Consellería de Cultura, Educación e Ordenación Universitaria, Spain (Axuda para Consolidación e Estructuración de unidades de investigación competitivas do Sistema Universitario de Galicia, Xunta de Galicia ED431C 2017/17 & Centro singular de investigación de Galicia acreditación 2019–2022, Spain , ED431G 2019/03 ) and the European Regional Development Fund (ERDF) is gratefully acknowledged. D. F-C. thanks Xunta de Galicia, Spain for financial support through a postdoctoral grant. This work was supported in part by the U.S. Department of Energy , Office of Science, Office of Basic Energy Sciences under Award DE-SC0015997.
© 2020 Elsevier B.V.
- Dual-level direct-dynamics calculations
- Kinetic Monte Carlo
- Minimum energy path
- Multidimensional tunneling
- Multipath variational transition state theory
- Multiple conformations
- Reaction mechanisms
- Variational transition state theory