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Eyringpy

eyringpy_logo.png

User-friendly program

Eyringpy is a program designed to compute rate constants using Transition State Theory (TST) and Variational Transition State Theory (VTST), both in the gas phase and in solution. The Gibbs activation energy is obtained from canonical partition functions calculated from first principles. The program supports unimolecular and bimolecular reactions with one or two products. It can also estimate the rate constants of bimolecular reactions involving pre-reactive and/or product complexes. Reaction symmetry is included, and one-dimensional Wigner and Eckart tunneling corrections are available.

For solution-phase reactions, Eyringpy incorporates Collins–Kimball theory to account for diffusion limits, Marcus theory for electron transfer (ET) processes, and molar fractions to evaluate pH effects in aqueous media.

The latest version, Eyringpy, includes an IRC-Analysis module that monitors the evolution of primitive changes along the intrinsic reaction coordinate (IRC). Currently available analyses include bond distances, bond angles, Wiberg bond indices, natural charges, dipole moments, orbital energies and related properties, as well as reaction forces.

To improve accuracy, energy profiles are smoothed using a spline interpolator from Python’s SciPy library, while a discriminator removes noisy data points. Visualization of the evolution of primitive changes is performed with Python’s Matplotlib library.

eyringpy_functions.png

Compatibility

Eyringpy is compatible with Gaussian output files. Since version 2.1, compatibility has been extended to ORCA output files as well. Eyringpy 3.0 is available for Windows, macOS, and Linux:

  • Windows (64-bit): Windows 10 or 11

  • MacOS: OS X 10.11 (El Capitan) or later

  • Linux (64-bit): Distributions based on Ubuntu 22.04 LTS or newer (requires glibc 2.7 or higher)

Download Eyringpy 3.0

To obtain a copy, please complete the registration form. You will then receive access to the binary files compatible with your operating system.
 
[Download Eyringpy 3.0]

Old versions

Eyringpy 2.1

  • Windows (64-bit version): Windows 10 y 11

  • MacOS: OS X 10.14 (Mojave) and later

[Download Eyringpy 2.1]

Eyringpy 2.0

Available for the 64 bits version of:

 

  • Windows (64-bit): Windows 10 y 11

  • MacOS: OS X 10.11 (El Capitan) and later

  • Linux (64-bit): Ubuntu 18.04 and later

[Download Eyringpy 2.0]​​

Citation

Contact

For more information, bug reports, or suggestions for improving Eyringpy, please contact us at eyringpy2018@gmail.com.


When reporting issues, describe the problem in detail and attach the relevant output files (*.out or .log) along with the input file (.eif) used.

Dra. Eugenia Dzib

e-mail: eugenia.dzib@cinvestav.mx

            eugeniadzib@gmail.com

Dr. Filiberto Ortíz Chi

e-mail: fortiz@conacyt.mx

            fortiz666@gmail.com

Dr. Alan Quintal

e-mail: alan.quintal@cinvestav.mx

            alanquintal22@gmail.com

Dr. Gabriel Merino

e-mail: gmerino@cinvestav.mx

            gabriel.merino2@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. 


16. Amić, A.; Milenković, D.; Marković, J. D.; Marković, Z. J. Serb. Soc. Comput. Mech. 2020, 45. 


17. Arrué, L.; Pino‐Rios, R. J. Comput. Chem. 2020, 120


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

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