Exploring Intermolecular and Intramolecular Interactions: A Review beyond Hydrogen Bonds
DOI:
https://doi.org/10.29356/jmcs.v68i4.2306Keywords:
Hydrogen bonds, Electron density, QTAIM, Non-covalent interactionsAbstract
Intermolecular interactions have great relevance in the stability of chemical systems. The most studied non-covalent interactions are hydrogen bonds, but they are not the only ones. Dihydrogen bonds or hydrogen - hydrogen contacts, as well as those that occur between heteroatoms, have also shown to play an important role in the molecular structure of biomolecules, solids, surfaces and other chemical systems. In this article we summarize the main contributions of our group to the study of these intermolecular interactions.
Among the most important results generated in our group is the estimation of the interaction energy of the unconventional hydrogen bond C-H•••O, which showed its relevance in various systems. In addition, software programmed on graphic processing units was created in our group to analyze electron density using the Quantum Theory of Atoms in Molecules (QTAIM). This code has allowed us to study non-covalent interactions in large systems.
Resumen. Las interacciones intermoleculares tienen una gran relevancia en la estabilidad de sistemas químicos. Las más estudiadas son los puentes de hidrógeno, pero no han sido las únicas. Los enlaces dihidrógeno o los contactos hidrógeno-hidrógeno, así como las interacciones que ocurren entre heteroátomos, también han mostrado un papel importante en la estructura molecular de biomoléculas, sólidos, superficies y otros sistemas químicos. En este artículo resumimos las principales contribuciones de nuestro grupo hacia el estudio de estas interacciones intermoleculares.
Entre los resultados más importantes generados por nuestro grupo es la estimación de la energía de interacción de puentes de hidrógeno no convencionales C-H•••O, los cuales han mostrado su relevancia en varios sistemas. Además, el código computacional programado sobre tarjetas gráficas creado en nuestro grupo permite analizar la densidad electrónica usando la teoría cuántica de átomos en moléculas (QTAIM). Este código computacional nos ha permitido estudiar interacciones no covalentes en sistemas de gran tamaño.
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References
Jeffrey, G.A.; Saenger, W. Hydrogen bonding in Biological Structures. Springer- Verlag, 1991. DOI: https://doi.org/10.1007/978-3-642-85135-3
IUPAC Compendium of Chemical Terminology, 2nd ed., Royal Society of Chemistry, Cambridge, 1997. The online version (http://old.iupac.org/publications/compendium/) mostly corresponds to the second edition, compiled by A. D. McNaught and A. Wilkinson of the Royal Society of Chemistry. The definition of the term hydrogen bond is given at https://goldbook.iupac.org/terms/view/H02899.
Gautam, R. D. Angew. Chem. Int. Ed. 2011, 50, 52 – 59. DOI: /https://doi.org/10.1002/anie.201002960. DOI: https://doi.org/10.1002/anie.201190108
Richardson, T. B.; Koetzle, T. F.; Crabtree, R. H. Inorganica Chim. Acta 1996, 250, 69–73. DOI: https://doi.org/10.1016/S0020-1693(96)05212-7. DOI: https://doi.org/10.1016/S0020-1693(96)05212-7
Klooster, W. T.; Koetzle, T. F.; Siegbahn, P. E.; Richardson, T. B.; Crabtree, R. H. J. Am. Chem. Soc. 1999, 7, 6337–6343. DOI: https://doi.org/10.1021/acs.inorgchem.5b00927. DOI: https://doi.org/10.1021/ja9825332
Novoa, J. J.; Whangbo, M. H.; Williams, J. M. J. Chem. Phys. 1991, 94, 4835–4841.DOI: https://doi.org/10.1063/1.460568. DOI: https://doi.org/10.1063/1.460568
Matta, C. F.; Hernández-Trujillo, J.; Tang, T. H.; Bader, R. F. Chem. - Eur. J. 2003, 9,1940–1951. DOI: https://doi.org/10.1002/chem.200204626. DOI: https://doi.org/10.1002/chem.200204626
Alkorta, I.; Elguero, J.; Frontera, A. Crystals, 2020, 10,180-208. DOI: https://doi.org/10.3390/cryst10030180. DOI: https://doi.org/10.3390/cryst10030180
Jeffrey, G.A. An introduction to Hydrogen Bonding. Oxford University Press, 1997.
Vargas, R.; Garza, J.; Dixon, D. A.; Hay, B.P. J. Am. Chem. Soc. 2000, 122, 4750- 4755. DOI: https://doi.org/10.1021/ja993600a DOI: https://doi.org/10.1021/ja993600a
Ramírez, J.-Z; Vargas, R.; Garza, J. J. Mex. Chem. Soc. 2008, 52, 31-35.
Jansen, H. B.; Ross, P. Chem. Phys. Lett. 1969, 3, 140-143. DOI: https://doi.org/10.1016/0009-2614(69)80118-1. DOI: https://doi.org/10.1016/0009-2614(69)80118-1
Boys, S. B.; Bernardi, F. Mol. Phys. 1970, 19, 533. DOI: https://doi.org/10.1080/00268977000101561. DOI: https://doi.org/10.1080/00268977000101561
(a) Mayer, I.; Surjan, P. R. Chem. Phys. Lett. 1992, 191, 497-499. DOI: https://doi.org/10.1016/0009-2614(92)85415-7. (b) Simon, S.; Duran, M.; Dannenberg, J. J. J. Chem. Phys. 1996, 105, 11024-11031. DOI: https://doi.org/10.1063/1.472902. (c) Salvador, P.; Paizs, B.; Duran, M.; Suhai, S. J. Comput. Chem. 2001, 22, 765-786. DOI: https://doi.org/10.1002/jcc.1042.
Garza, J.; Ramírez, Z.; Vargas, R. J. Phys. Chem. A, 2005, 109, 643-651. DOI: https://doi.org/10.1021/jp046492+. DOI: https://doi.org/10.1021/jp046492+
Bader, R. F. W. Acc. Chem. Res. 1985, 18, 9-15. DOI: https://doi.org/10.1021/ar00109a003. DOI: https://doi.org/10.1021/ar00109a003
Kohout, M.; Savin, A. Int. J. QuantumChem. 1996, 60, 875-882. DOI: https://doi.org/10.1002/(SICI)1097-461X(1996)60:4<875::AID-QUA10>3.0.CO;2-4. DOI: https://doi.org/10.1002/(SICI)1097-461X(1996)60:4<875::AID-QUA10>3.0.CO;2-4
Navarrete-López, A. M.; Garza, J.; Vargas, R. J. Phys. Chem. A 2007, 111, 11147- 11152. DOI: https://doi.org/10.29356/jmcs.v52i1.1043. DOI: https://doi.org/10.1021/jp074592k
Hernández-Esparza, R.; Mejía-Chica, S.-M.; Zapata-Escobar, A. D.; Guevara-García, A.; Martínez-Melchor, A.; Hernández-Pérez, J.-M.; Vargas, R; Garza, J. J. Comput. Chem. 2014, 35, 2272-2278. DOI: https://doi.org/10.1002/jcc.23752. DOI: https://doi.org/10.1002/jcc.23752
Hernández-Esparza, R.; Vázquez-Mayagoitia, A.; Soriano-Agueda, L. A.; Vargas, R.; Garza, J. Int. J. Quantum Chem. 2018, 119, e25671. DOI: https://doi.org/10.1002/qua.25671. DOI: https://doi.org/10.1002/qua.25671
Cruz, J. C.; Hernández-Esparza, R.; Vázquez-Mayagoitia, A.; Vargas, R. Garza, J. J. Chem. Inf. Model. 2019, 59, 3120-3127. DOI: https://doi.org/10.1021/acs.jcim.8b00951. DOI: https://doi.org/10.1021/acs.jcim.8b00951
Cruz, J. C.; García-Gutierrez, P.; Zubillaga, R. A.; Vargas, R.; Garza, J. in: Frontiers in Computational Chemistry. Vol. 5, Ul-Haq, Z.; Wilson, A. K. Ed., Bentham Science Publishers, 2020, 149-173. DOI: https://doi.org/10.2174/9789811457791120050006. DOI: https://doi.org/10.2174/9789811457791120050006
García-Gutiérrez, P.; Zubillaga, R. A.; Ibarra, I. A.; Martínez, A.; Vargas,R.; Garza, J. C.S.B.J. 2021, 19, 4669–4675. DOI: https://doi.org/10.1016/j.csbj.2021.08.015. DOI: https://doi.org/10.1016/j.csbj.2021.08.015
Martínez, A.; García-Gutiérrez, P.; Zubillaga, R. A.; Garza, J.; Vargas, R. Phys. Chem. Chem. Phys. 2021, 23, 14224-14230. DOI: https://doi.org/10.1039/D1CP01637 . DOI: https://doi.org/10.1039/D1CP01637G
Padilla‑Bernal, G.; Vargas, R.; Martínez, A. Theor. Chem. Acc. 2023, 142:65. DOI: https://doi.org/10.1007/s00214-023-03016-6. DOI: https://doi.org/10.1007/s00214-023-03016-6
Martínez, A.; Ibarra, I. A.; Vargas, R. Plos ONE 2019, 14, e0224691. DOI: https://doi.org/10.1371/journal.pone.0224691. DOI: https://doi.org/10.1371/journal.pone.0224691
Goode-Romero, G. Domínguez, L.; Vargas, R.; Ibarra, I. A.; Martínez, A. Comput. Theor. Chem. 2020, 1197, 113125(1-6). DOI: https://doi.org/10.1016/j.comptc.2020.113125. DOI: https://doi.org/10.1016/j.comptc.2020.113125
Goode-Romero, G.; Winnberg, U.; Domínguez, L.; Ibarra, I. A.; Vargas, R.; Winnberg, E.; Martínez, A. Scientific Reports 2020, 10, 21581. DOI: https://doi.org/10.1038/s41598-020- 78446-4. DOI: https://doi.org/10.1038/s41598-020-78446-4
Santillán-Vargas, H.; Ramírez, J. Z.; Garza, J.; Vargas, R. Int. J Quantum Chem. 2012, 112, 3587–3593. DOI: https://doi.org/10.1002/qua.24225. DOI: https://doi.org/10.1002/qua.24225
Nieto-Malagón, G.; Hernández-Pérez, J.; Vargas, R.; Garza, J. Int. J Quantum Chem. 2012, 112, 3552–3557. DOI: https://doi.org/10.1002/qua.24186. DOI: https://doi.org/10.1002/qua.24186
Bautista-Renedo, J.-M.; Cuevas-Yañez, E.; Reyes-Pérez, H.; Vargas, R; Garza, J.; González-Rivas, N. RSC Adv. 2020, 10, 20202-20210. DOI: https://doi.org/10.1039/C9RA10218C. DOI: https://doi.org/10.1039/C9RA10218C
Bautista-Renedo, J.-M.; Hernández-Esparza, R.; Cuevas-Yañez, E.; Reyes-Pérez, H.; Vargas, R.; Garza, J.; González-Rivas, N. Int. J Quantum Chem., 2022, e26859. DOI: https://doi.org/10.1002/qua.26859. DOI: https://doi.org/10.1002/qua.26859
Vargas, R.; Garza, J.; Hay, B. P.; Dixon, D. A. J. Phys.Chem. A, 2002, 106, 3213- 3218. DOI: https://doi.org/10.1021/jp013952f. DOI: https://doi.org/10.1021/jp013952f
Bustos-Terrones, V.; Serratos, I. N.; Vargas, R.; Landeros-Rivera, Bruno. C.; Bustos- Terrones, Y. A.; Soto Estrada, A. M.; Vicente Escobar, J. O.; Romero Romo, M. A.; Uruchurtu, J.; Menchaca, C.; Esparza Schulz, J. M.; Domínguez, A. ChemistryOpen, 2018, 7, 984-994. DOI: https://doi.org/10.1002/open.201800201. DOI: https://doi.org/10.1002/open.201800201
Salazar-Cano, J.-R.; Guevara-García, A.; Vargas, R.; Restrepo, A; Garza, J. Phys. Chem. Chem. Phys. 2016, 18, 23508-23515. DOI: https://doi.org/10.1039/C6CP04086A. DOI: https://doi.org/10.1039/C6CP04086A
García-Hernández, E.; Flores-Moreno, R.; Vázquez-Mayagoitia, A.; Vargas, R.; Garza, J. New J. Chem. 2017, 41, 965-974. DOI: https://doi.org/10.1039/C6NJ02655A. DOI: https://doi.org/10.1039/C6NJ02655A
García, J.-J.; Hernández-Esparza, R.; Vargas, R.; Tiznado, W.; Garza, J. New J. Chem. 2019, 43, 4309-4650. DOI: https://doi.org/10.1039/C8NJ06315J. DOI: https://doi.org/10.1039/C8NJ06315J
Monjaraz-Rodríguez, A.; Rodriguez-Bautista, M.; Garza, J.; Zubillaga, R. A.; Vargas, R. J. Mol. Model. 2018, 24, 187-195. DOI: https://doi.org/10.1007/s00894-018-3725-5. DOI: https://doi.org/10.1007/s00894-018-3725-5
Ramírez, J.-Z.; Vargas, R.; Padilla-Martínez, I.; Flores-Huerta, A. G.; Garza, J. J. Mex. Chem. Soc. 2012, 56, 275-278.
Guillén-Villar, R. C.; Vargas-Álvarez, Y.; Vargas, R.; Garza, J.; Matus, M. H.; Salas-Reyes, M.; Domínguez, Z. J. Electroanal. Chem. 2015, 740, 95–104. DOI: https://doi.org/10.1016/j.jelechem.2015.01.003. DOI: https://doi.org/10.1016/j.jelechem.2015.01.003
Gómez, M.; González, I.; González, F. J.; Vargas, R.; Garza, J. Electrochem. Comm. 2003, 5, 12-15. DOI: https://doi.org/10.1016/S1388-2481(02)00519-2. DOI: https://doi.org/10.1016/S1388-2481(02)00519-2
García-Hernández, E.; Garza, J. J. Mex. Chem. Soc. 2017, 61, 222-228. DOI: https://doi.org/10.29356/jmcs.v61i3.348
Badillo-Ramírez, I.; Landeros-Rivera, B.; de la O-Cuevas, E.; Vargas, R.; Garza, J.; Saniger, J. M. New J. Chem. 2019, 43, 15861-15870. DOI: https://doi.org/10.1039/C9NJ03781K. DOI: https://doi.org/10.1039/C9NJ03781K
Ortega-Moo, C.; Garza, J.; Vargas, R. Theor. Chem. Acc. 2016, 135, 177-189. DOI: https://doi.org/10.1007/s00214-016-1932-7. DOI: https://doi.org/10.1007/s00214-016-1932-7
Ortega-Moo, C.; Durán, R.; Herrera, B.; Gutiérrez-Oliva, S.; Toro-Labbe, A.; Vargas, R. Phys. Chem. Chem. Phys. 2017, 19, 14512-14519. DOI: https://doi.org/10.1039/c7cp01304c. DOI: https://doi.org/10.1039/C7CP01304C
Gutiérrez-Flores, J.; Huerta, E. H.; Cuevas, G.; Garza, J.; Vargas, R. J. Org. Chem. 2024, 89, 257. DOI: https://doi.org/10.1021/acs.joc.3c02016. DOI: https://doi.org/10.1021/acs.joc.3c02016
Padilla-Bernal, G.; Gutiérrez-Flores, J.; Garza, J.; Vargas R. Theor. Chem. Acc. 2023, 142, 42. DOI: https://doi.org/10.1007/s00214-023-02978-x. DOI: https://doi.org/10.1007/s00214-023-02978-x
González-Martínez, G. A.; Jurado-Vázquez, T.; Solís-Ibarra, D.; Vargas, B.; Sánchez-González, E.; Martínez, A.; Vargas, R.; González-Zamora, E.; and Ibarra, I. A. Dalton Trans. 2018, 47, 9459-9465. DOI: https://doi.org/10.1039/C8DT01369A. DOI: https://doi.org/10.1039/C8DT01369A
Sánchez-Bautista, J. E; Landeros-Rivera, B.; Jurado-Vázquez, T.; Martínez, A.; González-Zamora, E.; Balmaseda, J.; Vargas, R.; Ibarra, I. A. Dalton Trans. 2019, 48, 5176-5182. DOI: https://doi.org/10.1039/C9DT00384C. DOI: https://doi.org/10.1039/C9DT00384C
Lara-García, H. A.; Landeros-Rivera, B.; González-Zamora, E.; Aguilar-Pliego, J.; Gómez-Cortés, A.; Martínez, A.; Vargas, R.; Díaz, G.; Ibarra, I. A. Dalton Trans. 2019, 48, 8611-8616. DOI: https://doi.org/10.1039/C9DT01266D. DOI: https://doi.org/10.1039/C9DT01266D
Barrios-Vargas, L. J.; Ruiz-Montoya, J. G.; Landeros-Rivera, B.; Álvarez, J. R.; Alvarado-Alvarado, D.; Vargas, R.; Martínez, A.; González-Zamora, E.; Cáceres, L. M.; Morales, J. C.; Ibarra, I. A. Dalton Trans. 2020, 49, 2786-2793. DOI: https://doi.org/10.1039/C9DT04667D. DOI: https://doi.org/10.1039/C9DT04667D
Landeros-Rivera, B.; Ibarra, I. A.; Díaz, M.; Vargas, R.; Lara-García, H. A.; Garza, J.; Martínez, A.. Phys. Chem. Chem. Phys. 2020, 22, 7969-7974. DOI: https://doi.org/10.1039/D0CP00579G. DOI: https://doi.org/10.1039/D0CP00579G
Garrido-Olvera, L. P; Sanchez-Bautista, J. E.; Alvarado-Alvarado, D.; Landeros- Rivera, B.; Álvarez, J. R.; Vargas, R.; González-Zamora, E.; Balmaseda, J.; Lara- García, H. A.; Martínez, A.; Ibarra, I. A. RSC Adv. 2019, 9, 32864-32872. DOI: https://doi.org/10.1039/c9ra05991a. DOI: https://doi.org/10.1039/C9RA05991A
Rivera-Almazo, M.; Díaz-Ramírez, M. L.; Hernández-Esparza, R.; Vargas, R.; Martínez, A.; Martis, V.; Sáenz-Cavazos, P. A.; Williams, D.; Lima, E.; Ibarra, A.; Garza, J. Phys. Chem. Chem. Phys. 2021, 23 1454-1463. DOI: https://doi.org/10.1039/D0CP04668J. DOI: https://doi.org/10.1039/D0CP04668J
Díaz-Ramírez, M. L.; Vargas, B.; Álvarez, J. R.; Landeros-Rivera, B.; Rivera- Almazo, M.; Ramos, C.; Flores, J. G.; Morales, E.; Vargas, R.; Garza, J.; González-Zamora, E.; Martínez, A.; Solís-Ibarra, D.; Ibarra, I. A. Dalton Trans. 2020, 49, 6572-6577. DOI: https://doi.org/10.1039/D0DT00945H. DOI: https://doi.org/10.1039/D0DT00945H
Rivera-Almazo, M.; Pérez-Sánchez, E.; Martínez-Ahumada, E.; Martínez, A.; Garza, J.; Ibarra, I. A.; Vargas, R. J. Phys. Chem. C 2022, 126, 6465-647. DOI: https://doi.org/10.1021/acs.jpcc.2c00742. DOI: https://doi.org/10.1021/acs.jpcc.2c00742
Medel, E.; Obeso, J. L.; Serrano-Fuentes, C.; Garza, J.; Ibarra, I. A.; Leyva, C.; Inge, K. A.; Martínez, A.; Vargas, R. Chem. Comm. 2023, 59, 8684-8687. DOI: https://doi.org/10.1039/D3CC02304D. DOI: https://doi.org/10.1039/D3CC02304D
Medel, E.; Garza, J.; Ibarra, I. A.; Martínez, A.; Vargas, R. Comput. Theor. Chem. 2023, 1228, 114265. DOI: https://doi.org/10.1016/j.comptc.2023.114265. DOI: https://doi.org/10.1016/j.comptc.2023.114265
García-Revilla, M. A.; Cortés-Guzmán, F.; Rocha-Rinza, T.; Hernández-Trujillo, J. Int. J. Quantum Chem. 2019, 119, e25789. DOI: https://doi.org/10.1002/qua.25789. DOI: https://doi.org/10.1002/qua.25789
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