Recent News

Eyringpy

Eyringpy is a user-friendly program for performing thermochemical and kinetic calculations and analyzing the evolution of chemical properties along the intrinsic reaction coordinate. This code is written in Python and its most important features are a user-friendly interface and a simple input format. Eyringpy version 2.0 is formed by two main modules: Kinetics and IRC-Analysis. It is compatible with Linux, MacOS X, and Windows.

Kinetics is used for calculating thermochemical properties and rate constants for reactions in the gas phase and solution. Unimolecular and bimolecular systems with one and two products are supported. Thermochemical properties are estimated through canonical ensemble and rate constants are computed according to the transition state theory. One-dimensional Wigner and Eckart tunneling corrections are also available. Rate constants of bimolecular reactions involving the formation of pre-reactive complexes are also estimated. Eyringpy introduces specific methods to correct rate constants for reactions in solution, the Collins-Kimball theory to include the diffusion-limit, the Marcus theory for electron transfer processes, and the molar fractions to account for the solvent pH effect.

Rate constants for the reaction CH4 + Cl· → CH3· + HCl, in the range 200-300 K: (a) without corrections, (b) including Wigner correction, (c) including Eckart correction, and (d) experimental values.

Influence of the pH on the rate constants for the reaction NH3 + OH· → NH2· + H2O calculated at 298.15 K, including the diffusion and Eckart tunneling effect corrections.

IRC-Analysis monitors the evolution of chemical properties along the intrinsic reaction coordinate, such as bond lengths, angles, Wiberg bond indices, natural charges, orbital energies, and dipole moment, including the reaction force. The reaction force analysis is performed using the Reaction Force theory proposed by Toro-Labbé. A spline interpolator is available to smooth energy and reaction force profiles and also a plotter to visualize the evolution of the properties.

reaction_force.png

The V(ξ) (kcal mol-1), and F(ξ) (kcal mol-1 ξ-1) profiles of the degenerate [3,3] Cope rearrangement of 1,5-hexadiene from the reaction force analysis.

geometrical analysis.png

Structural profiles of the double group transfer between ethane and ethylene: (a) distance evolution between the carbon atoms forming/breaking double bonds, (b) distance evolution between the donor and acceptor carbon atoms and the transferred hydrogens, and (c) angle evolution between the hydrogens and the donor and acceptor carbon atoms.

For further details about Eyringpy and its methods please see the paper:

    

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 Solution" Int. J. Quantum Chem. 2019, 119, e25686.     

Download

 

Eyringpy 2.0 is available for downloading through the Merino Research Group at Cinvestav. To obtain a copy of Eyringpy you should fill out a form and send it to eyringpy2018@gmail.comor Professor Gabriel Merino, or Eugenia Dzib, or Alan Quintal. Then you will receive an executable compatible with the operating system you need.

 

Please download the order form here

Documentation

 

The Eyringpy user’s manual can be download here.

Citation

 

Please cite the next references:

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

    

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 Solution" Int. J. Quantum Chem2019, 119, e25686   

                                         

E. Dzib, J. L. Cabellos, F. Ortiz-Chi, S. Pan, G. Merino, Eyringpy 1.0, Cinvestav, Merida, Yucatan 2018.

Contact

 

For further information about Eyringpy, to report bugs and comments about the manual or the web page, please contact us via eyringpy2018@gmail.com:

 

Professor Gabriel Merino

e-mail: gmerino@cinvestav.mx

            gabriel.merino2@gmail.com

M. Sc. Eugenia Dzib

e-mail: eugenia.dzib@cinvestav.mx

            eugeniadzib@gmail.com

M. Sc. Alan Quintal

e-mail: alan.quintal@cinvestav.mx

            alanquintal22@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