Eyringpy

eyringpy_logo.png

User-friendly program

Eyringpy is a program for computing rate constants using the transition state theory (TST), in the gas phase and in solution. The Gibbs activation energy is obtained by computing from scratch the canonical partition functions. Unimolecular and bimolecular reactions with one or two products are supported. Rate constants of bimolecular reactions involving the formation of pre-reactive and/or product complexes are also estimated. The reaction symmetry is considered. One-dimensional Wigner and Eckart tunneling corrections are also available. To compute rate constants in solution, Eyringpy employs the Collins–Kimball theory to include the diffusion-limit, the Marcus theory for electron transfer (ET) processes, and the molar fractions to account for the effect of pH in aqueous reactions. Two versions are available.

In Eyringpy2.0, the IRC-Analysis is available for monitoring the evolution of primitive changes along the intrinsic reaction coordinate (IRC). For now, the available primitive changes that can be studied are the bond distances, angles, Wiberg bond indices, natural charges, dipole moment, orbital energies (and related properties), and reaction forces. A spline interpolator from Python's Scipy library is used to smooth the energy profiles. In addition, a discriminator to remove points causing noise in the energy profiles is also available. The Python's Matplotlib library is used for plotting the evolution of the primitive changes along the IRC.

How to download Eyringpy?

Eyringpy is available for Windows, macOS X, and Linux. To obtain a copy you should fill out the form. Then you will be able for downloading the binary compatible with the required operating system.

  • Download Eyringpy2.0 here

Compatibility

Eyringpy2.0

Available for the 64 bits version of:

 

  • Windows: Windows 10

  • macOS: OS X 10.11 (El Capitan) and higher versions

  • Linux: Ubuntu 18.04 based Linux Distributions and higher versions

* For Linux it is mandatory to have the library Glibc 2.7 or a higher version installed.

Citation

If you publish results obtained with Eyringpy in the scientific literature, please include the references as follows:

∗ General references:

1. E. Dzib, A. Quintal, F. Ortiz-Chi, G. Merino, Eyringpy 2.0, Cinvestav, Merida, Yucatan 2021.

∗ If you compute rate constants also cite:

2. E. Dzib, J. L Cabellos, F. Ortíz-Chi, S. Pan, A. Galano, G. Merino, Eyringpy: A Program for computing  Rate Constants in the Gas Phase and in SolutionInt. J. Quantum Chem2019, 119, e.25686.

* If you perform the analysis of primitive changes along the IRC also cite: 

3. A. Quintal, E. Dzib, F. Ortiz-Chi, P. Jaque, A. Restrepo, and G. Merino, Automating the IRC Analysis within Eyringpy. Int. J. Quantum Chem. 2021, e26684.

Contact

For more information about Eyringpy, to report bugs, and send questions or suggestions for improving its performance, please contact us via eyringpy2018@gmail.com. If you want to report bugs or errors, please describe your problem in detail and send us the output files (*.out or *.log) with the electronic structure results and the input file (*.eif) you are using.

Professor Filiberto Ortíz Chi

e-mail: fortiz@conacyt.mx

            fortiz666@gmail.com

Papers citing Eyringpy

1. Gómez, S.; Restrepo, A. Phys. Chem. Chem. Phys. 2019, 21, 15815. 


2. Llano, S.; Gómez, S.; Londoño, J.; Restrepo, A. Phys. Chem. Chem. Phys. 2019, 21, 3752. 


3. Machado, H. G.; Sanches-Neto, F. O.; Coutinho, N. D.; Mundim, K. C.; Palazzetti, F.; Carvalho-Silva, V. H. Molecules 2019, 24, 3478


4. Merino, G.; Muñoz‐Castro, A.; Nascimento, M. A. C.; Vela, A. Int. J. Quantum Chem. 2019, 119, e25852. 


5. Ngo, T. C.; Nguyen, T. H.; Dao, D. Q. J. Chem. Inf. Model. 2019, 59, 766


6. Thong, N. M.; Vo, Q. V.; Huyen, T. L.; Bay, M. V.; Tuan, D.; Nam, P. C. ACS omega 2019, 4, 14996. 


7. Van Quan, V.; Phu, H. T.; Thao, P. T. T.; Nam, P. C. Vietnam J. Chem. 2019, 57, 728. 


8. Vásquez-Espinal, A.; Yañez, O.; Osorio, E.; Areche, C.; García-Beltrán, O.; Ruiz, L. M.; Cassels, B. K.; Tiznado, W. Front. Chem. 2019, 7, 818. 


9. Vo, Q. V.; Mechler, A. J. Chem. Inf. Model. 2019, 60, 316


10. Vo, Q. V.; Nam, P. C.; Thong, N. M.; Trung, N. T.; Phan, C.-T. D.; Mechler, A. ACS omega 2019, 4, 8935


11. Vo, Q. V.; Nam, P. C.; Van Bay, M.; Thong, N. M.; Hieue, L. T.; Mechler, A. RSC Adv. 2019, 9, 42020


12. Vo, Q. V.; Van Bay, M.; Nam, P. C.; Mechler, A. J. Phys. Chem. B 2019, 123, 7777


13. Vo, Q. V.; Van Bay, M.; Nam, P. C.; Mechler, A. ACS omega 2019, 4, 19375. 


14. Vo, Q. V.; Van Gon, T.; Van Bay, M.; Mechler, A. J. Phys. Chem. B 2019, 123, 10672. 


15. Wei, W.; Ma, J.; Xie, D.; Zhou, Y. RSC Adv. 2019, 9, 13776. 


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18. Bay, M. V.; Nam, P. C.; Quang, D. T.; Mechler, A.; Hien, N. K.; Hoa, N. T.; Vo, Q. V. ACS omega 2020, 5, 7895. 


19. Boulebd, H.; Khodja, I. A.; Bay, M. V.; Hoa, N. T.; Mechler, A.; Vo, Q. V. J. Phys. Chem. B 2020, 124, 4123. 


20. Boulebd, H.; Mechler, A.; Hoa, N. T.; Vo, Q. V. New J. Chem. 2020, 44, 9863. 


21. Boulebd, H.; Tam, N. M.; Mechler, A.; Vo, Q. V. New J. Chem. 2020, 44, 16577. 


22. Dao, D. Q.; Phan, T. T. T.; Nguyen, T. L. A.; Trinh, P. T. H.; Tran, T. T. V.; Lee, J. S.; Shin, H. J.; Choi, B.-K. J. Chem. Inf. Model. 2020, 60, 1329. 


23. Djefoulna, V. H. H.; Fifen, J. J.; Malloum, A.; Jaidane, N.-E. Theor. Chem. Acc. 2020, 139, 1. 


24. Hoa, N. T.; Van Bay, M.; Mechler, A.; Vo, Q. V. ACS omega 2020, 5, 17715. 


25. Huong, D. Q.; Duong, T.; Nam, P. C. Hue Univ. J. Nat. Sci. 2020, 129, 5. 


26. Minh, T. N. Vietnam J. Sci. Technol. 2020, 58, 565


27. Thao, P. T. T.; Tran, B. T.; Thong, N. M.; Quang, D. T.; Hien, N. K.; Nguyen, M. T.; Nam, P. C. ACS omega 2020, 5, 27572. 


28. Vo, Q. V.; Bay, M. V.; Nam, P. C.; Quang, D. T.; Flavel, M.; Hoa, N. T.; Mechler, A. J. Org. Chem. 2020.

 
29. Vo, Q. V.; Hoa, N. T. RSC Adv. 2020, 10, 36843. 


30. Vo, Q. V.; Hoa, N. T.; Nam, P. C.; Quang, D. T.; Mechler, A. ACS omega 2020, 5, 24106. 


31. Vo, Q. V.; Tam, N. M.; Van Bay, M.; Mechler, A. Chem. Phys. Lett. 2020, 739, 137004. 


32. Vo, Q. V.; Tam, N. M.; Hieu, L. T.; Van Bay, M.; Thong, N. M.; Le Huyen, T.; Hoa, N. T.; Mechler, A. RSC Adv. 2020, 10, 14937. 


33. Vo, Q. V.; Thong, N. M.; Le Huyen, T.; Nam, P. C.; Tam, N. M.; Hoa, N. T.; Mechler, A. RSC Adv. 2020, 10, 20089. 

34. Thao, P. T. T.; Thong, N. M.; Vo, Q. V.; Van Bay, M.; Quang, D. T.; Nam, P. C., Vietnam J. Chem. 2020, 58, 742.

35. Boulebd, H., Phytochemistry 2021, 184, 112670.

36. Buelna-Garcia, C. E.; Cabellos, J. L.; Quiroz-Castillo, J. M.; Martinez-Guajardo, G.; Castillo-Quevedo, C.; de-Leon-Flores, A.; Anzueto-Sanchez, G.; Martin-del-Campo-Solis, M. F., Materials 2021, 14, 112.

37. Vásquez-Espinal, A.; Yañez, O.; Osorio, E.; Areche, C.; García-Beltrán, O.; Ruiz, L. M.; Cassels, B. K.; Tiznado, W., New J. Chem. 2021, 45, 590.

38. Vo, Q. V.; Hoa, N. T.; Mechler, A., Polym. Degrad. Stab. 2021, 185, 109483