Publications

17. J. Mojica Sánchez, H. Gonzalez Ramirez, J. Nochebuena, G. Ruiz Ibarra, V. Medel Juárez. Metal-Doped Graphene as Adsorbents for Glyphosate: A DFT and Molecular Dynamics Approach. Australian Journal of Chemistry 2026; CH25136.

16. J. Arcudia, J. Nochebuena, and G. A. Cisneros. Extending QM/GEM Capabilities: Geometry Optimization and Multipoles Applied to Molecular Cooperativity Studies. ChemRxiv. 2025.

15. E. García-Hernández, F. J. Torres, D. Cortés-Arriagada, J. Nochebuena. Understanding the co-adsorption mechanism between nanoplastics and neonicotinoid insecticides from an atomistic perspective. J. Mol. Model. 2025, 31 (5), 140.

14. A. J. Etindele, A. Ponra, M. E. Casida, G. A. Cisneros, and J. Nochebuena. Theoretical Study of Reactivity Indices and Rough Potential Energy Curves for the Dissociation of 59 Fullerendiols in the Gas Phase and in Aqueous Solution with an Implicit Solvent Model. J. Phys. Chem. A 2025, 129, 2133–2143.

13. S. Chatterjee, J. Nochebuena, and G. A. Cisneros. Impact of an Ionic Liquid Solution on Horseradish Peroxidase Activity. J. Am. Chem. Soc. 2024, 146 (19), 13247–13257.

12. J. Nochebuena, A. C. Simmonett, G. A. Cisneros. Seamless Integration of GEM, a Density Based-Force Field, for QM/MM Simulations via LICHEM, Psi4, and Tinker-HP. J. Chem. Phys. 2024, 160 (17), 174103.

11. J. Nochebuena, S. Liu, and G. A. Cisneros. Relative Cooperativity in Neutral and Charged Molecular Clusters Using QM/MM Calculations. J. Chem. Phys. 2024, 160 (13), 134301.

10. J. Nochebuena, J.-P. Piquemal, S. Liu, G. A. Cisneros. Cooperativity and Frustration Effects (or Lack Thereof) in Polarizable and Non-Polarizable Force Fields. J. Chem. Theory Comput. 2023, 19 (21), 7715–7730.

9. J. Nochebuena and G. A. Cisneros. Polarizable MD and QM/MM Investigation of Acrylamide-Based Leads to Target the Main Protease of SARS-CoV-2. J. Chem. Phys. 2022, 157 (18), 185101.

8. J. P. Mojica-Sánchez, V. M. Langarica-Rivera, K. Pineda-Urbina, J. Nochebuena, G. K. Jayaprakash, Z. Gómez-Sandoval. Adsorption of Glyphosate on Graphene and Functionalized Graphenes: A DFT Study. Comput. Theor. Chem. 2022, 1215, 113840.

7. G. Mondragón-Solórzano, J. Sandoval-Lira, J. Nochebuena, G. A. Cisneros, and J. Barroso-Flores. Electronic Structure Effects Related to the Origin of the Remarkable Near-Infrared Absorption of Blastochloris Viridis’ Light Harvesting 1-Reaction Center Complex. J. Chem. Theory Comput. 2022, 18 (7), 4555–4564.

6. J. Nochebuena, L. Quintanar, A. Vela, and G. A. Cisneros. Structural and Electronic Analysis of the Octarepeat Region of Prion Protein with Four Cu2+ by Polarizable MD and QM/MM Simulations. Phys. Chem. Chem. Phys. 2021, 23 (38), 21568–21578.

5. J. Nochebuena, S. Naseem-Khan, and G. A. Cisneros. Development and Application of Quantum Mechanics/Molecular Mechanics Methods with Advanced Polarizable Potentials. WIREs Comput. Mol. Sci. 2021, 11 (4), e1515.

4. E. García-Hernández, L. Palomino-Asencio, R. Catarino-Centeno, J. Nochebuena, D. Cortés-Arriagada, and E. Chigo-Anota. In Silico Study of the Adsorption of Acetamiprid on Functionalized Carbon Nanocones. Phys. E 2021, 128, 114516. 

3. J. Nochebuena, C. Cuautli, and J. Ireta. Origin of Cooperativity in Hydrogen Bonding. Phys. Chem. Chem. Phys. 2017, 19 (23), 15256–15263.

2. J. Nochebuena and J. Ireta. On Cooperative Effects and Aggregation of GNNQQNY and NNQQNY Peptides. J. Chem. Phys. 2015, 143 (13), 135103.

1. J. Nochebuena, A. Ramírez, and J. Ireta. On the van der Waals Interactions and the Stability of Polypeptide Chains in Helical Conformations. Int. J. Quantum Chem. 2015, 115 (22), 1613–1620.