Publications

View Yamil J. Colón’s Google Scholar profile for a complete listing of citations and work

  1. E. Osaro, M. LaCapra, and Y. J. Colón* “Harmonizing Adsorption and Diffusion in Active Learning Campaigns of Gas Separations in a MOF”, J. Phys. Chem. C, 2025, 129, 21, 9877-9891. https://doi.org/10.1021/acs.jpcc.5c00922

  2. O. Mendible Barreto, J. K. Whitmer, and Y. J. Colón* “Considerations in the use of machine learning force fields for free energy calculations”, J. Chem. Phys., 2025, 162, 174119. https://doi.org/10.1063/5.0252043

  3. R. R. Bhawnani, O. Mendible Barreto, P. K. R. Podupu, Y. J. Colón,* G. Giri,* and M. R. Singh* “Next Generation Computational and Experimental Tools for Understanding Nucleation and Growth of Metal-Organic Frameworks”, ACS Materials Lett. 2025, 7, 906-927. https://doi.org/10.1021/acsmaterialslett.4c02600

  4. H. Jeon, T. M. Zanon, @J. Carpenter, Y. J. Colón, and Y. Wang “A Bioinert Hydrogel Framework for Precision 3D Cell Cultures: Advancing Automated High-Content and High-Throughput Drug Screening”, Small Science, 2025, 5 (4), 2400440. ttps://doi.org/10.1002/smsc.202400440

  5. J. Carpenter and Y. J. Colón* “Understanding Stable Adsorption States in Flexible Soft Porous Coordination Polymers through Free Energy Profiles”, Mol. Sys. Des. & Eng., 2025, 10, 194-204. https://doi.org/10.1039/D4ME00154K

  6. S. Raj and Y. J. Colón* “Free Energy Profiles of Monomeric Species in MOFs for Predicting Thermal Stability of MOF-Polymer Systems”, ACS Ind. & Eng. Chem. Research, 2024, 63, 50, 21901-21906. https://doi.org/10.1021/acs.iecr.4c03228

  7. E. Osaro, F. Fajardo-Rojas, G. Cooper, D.A. Gómez-Gualdrón, and Y. J. Colón* “Active learning of alchemical adsorption simulations; towards a universal adsorption model”, Chemical Science, 2024, 15, 17671-17684. https://doi.org/10.1039/D4SC02156H

  8. E. Osaro and Y. J. Colón* “Optimizing the Prediction of Adsorption in Metal-Organic Frameworks Leveraging Q-Learning”, AIChE Journal, 2024, e18611. https://doi.org/10.1002/aic.18611

  9. D. O. Abranches, W. Dean, M. Munoz, W. Wang, Y. Liang, B. Gurkan, E. Maginn, and Y. J. Colón* “Combining High Throughput Experiments and Active Learning to Characterize Deep Eutectic Solvents” ACS Sustainable Chemistry and Engineering, 2024, 12 (38), 14218-14229. https://doi.org/10.1021/acssuschemeng.4c04507

  10. Z. Wang, I. Pacheco-Fernández, @J. Carpenter, T. Aoyama, G. Huang, A. P. Isfahani, B. Ghalei, E. Sivaniah, K. Urayama, Y. J. Colón, and S. Furukawa “Pore-networked membrane using linked metal-organic polyhedral for trace-level pollutant removal and detection in environmental water” Nature Communications Materials, 2024, 5 (1), 161. https://doi.org/10.1038/s43246-024-00607-z

  11. S. Paiva. R. Fritz, +S. Raj, Y. J. Colón, and F. Herrera “Efficient Generation of Polarization-Entangled Photons in Metal-Organic Framework Waveguides” Optics Express, 2024, 32 (17), 29514-29525. https://doi.org/10.1364/OE.532747

  12. P. Verma, M. Bannon, M. Kuenen, +S. Raj, A. Dhakal, K. Stone, A. Nichols, C. Machan, Y. J. Colón, R. Letteri, and G. Giri, “Expanding the Design Space of Polymer-Metal Organic Framework (MOF) gels by understanding polymer-MOF interactions” Chemistry of Materials, 2024, 36 (19), 9356-9369. https://doi.org/10.1021/acs.chemmater.4c00112

  13. D. O. Abranches, E. J. Maginn, and Y. J. Colón*, “Stochastic Machine Learning via Sigma Profiles to Build a Chemical Design Space” Proceedings of the National Academy of Sciences, 2024, 121 (31), e2404676121. https://doi.org/10.1073/pnas.2404676121

  14. F. J. Carmona Esteva, Y. Zhang, E. J. Maginn*, and Y. J. Colón*, “Consistent and Reproducible Computation of the Glass Transition Temperature from Molecular Dynamics Simulations” J. Chem. Phys. 2024, 161, 1, 014108. https://doi.org/10.1063/5.0207835

  15. S. Raj, S. Paiva, R.A. Fritz, F. Herrera, and Y. J. Colón*, “First-principles screening of metal-organic frameworks for entangled photon generation” Materials for Quantum Technology, 2024, 4, 1, 015404. https://doi.org/10.1088/2633-4356/ad2c96

  16. D. O. Abranches, E. J. Maginn, and Y. J. Colón*, “Boosting Graph Neural Networks with Molecular Mechanics: A Case Study of Sigma Profile Prediction” Journal of Chemical Theory and Computation, 2023, 19, 24, 9318-9328. https://doi.org/10.1021/acs.jctc.3c01003

  17. K. Mukherjee, E. Osaro, and Y. J. Colón*, “Active learning for efficient navigation of multi-component gas adsorption landscapes in a MOF.” Dig. Discover., 2023, 2, 1506-1521. https://doi.org/10.1039/D3DD00106G

  18. K. Aruachan, Y. J. Colón, D. Aravena, and F. Herrera, “Semi-Empirical Haken-Strobl Model for Molecular Spin Qubits.” New J. of Phys. 2023, 25, 093031. https://doi.org/10.1088/1367-2630/acf2bd

  19. E. Osaro, K. Mukherjee, and Y. J. Colón*, “Active Learning for Adsorption Simulations: Evaluation, Criteria Analysis, and Recommendations for Metal-Organic Frameworks." Ind. Eng. Chem. Res. 2023, 62, 33, 13009-13024. https://doi.org/10.1021/acs.iecr.3c01589

  20. D. O. Abranches, E. J. Maginn, and Y. J. Colón*, “Activity coefficient acquisition with thermodynamics-informed active learning for phase diagram construction.” AIChE Journal, 2023, 69:e18141. https://doi.org/10.1002/aic.18141

  21. S. Raj, R. A. Fritz, F. A. Herrera, and Y. J. Colón*, “Understanding the Correlation Between Structure and Entangled Photon Pair Properties with Metal-Organic Frameworks.” J. Phys. Chem. C., 2023, 127, 23, 10987-10996. https://doi.org/10.1021/acs.jpcc.3c00355

  22. G. M. Cooper and Y. J. Colón*, “Metal-organic framework clustering through the lens of transfer learning.” Mol. Syst. Des. Eng., 2023, 8, 1049-1059. https://doi.org/10.1039/D3ME00016H

  23. J. Shi, F. Albreiki, Y. J. Colón, S. Srivastava, and J. K. Whitmer, “Transfer Learning Facilitates the Prediction of Polymer-Surface Adhesion Strength.” J. Chem. Theory and Comp., 2023, 19, 14, 4631-4640. https://doi.org/10.1021/acs.jctc.2c01314

  24. F. J. Carmona Esteva, Y. Zhang, Y. J. Colón*, E. J. Maginn*, “Molecular Dynamics Simulation of the Influence of External Electric Fields on the Glass Transition Temperature of the Ionic Liquid 1-Ethyl-3-methylimidazolium Bis(trifluoromethylsulfonyl)imide.” J. Phys. Chem. B, 2023, 127, 20, 4623-4632. https://doi.org/10.1021/acs.jpcb.3c00936

  25. T. Bikku, R. A. Frtiz, Y. J. Colón, and F. Herrera, “Machine Learning of Organic Compounds Using Visible Light.” J. Phys. Chem. A, 2023, 127, (10), 2407-2414. https://doi.org/10.1021/acs.jpca.2c07955

  26. J. Carpenter and Y. J. Colón*, “Atomistic simulation of soft porous coordination polymers.” J. Chem. Phys., 2023, 158, 7, 074901. https://doi.org/10.1063/5.0131179

  27. G. A. González, R. A. Fritz, Y. J. Colón, and F. Herrera, “Model reduction for molecular diffusion in nanoporous media.” Phys. Rev. Mat. 2023, 7, 3, 036001. https://doi.org/10.1103/PhysRevMaterials.7.036001

  28. D. A. Gómez-Gualdrón, C. M. Simon, and Y. J. Colón, “Efficient Data Utilization in Training Machine Learning Models for Nanoporous Materials Screening.” AI-Guided Design and Property Prediction for Zeolites and Nanoporous Materials, Book Chapter, Wiley, 2023, 343-376. https://doi.org/10.1002/9781119819783.ch13

  29. J. Gonzalez, K. Mukherjee, Y.J. Colón*, “Understanding structure-property relationships of MOFs for gas sensing through Henry’s constants.” J. Chem. Eng. Data, 2023, 68, 1, 291-302. https://doi.org/10.1021/acs.jced.2c00443

  30. J. Osterrieth, J. Rampersad, D. G. Madden, N. Rampal, L. Skoric, B. Connolly, M. Allendorf, V. Stavila, R. Ameloot, J. Marreiros, C. Ania, D. C. S. Azevedo, E. Vilarrasa-García, B. F. Santos, X. Bu, X. Zang, H. Bunzen, N. R. Champness, S. L. Griffin, B. Chen, R. Lin, B. Coasne, S. M. Cohen, J. Moreton, Y. J. Colón, L. Chen, R. Clowes, F. Coudert, Y. Cui, B. Hou, D. D’Alessandro, P. W. Doheny, M. Dinca, C. Sun, C. Doonan, M. Huxley, J. D. Evans, R. Ricco, O. Farha, K. B. Idrees, T. Islamoglu, P. Feng, H. Yang, R. Forgan, D. Bara, S. Furukawa, E. Sanchez, J. Gascon, S. Telalovic, S. K. Ghosha, M. R. Hill, M. M Sadiq, P. Horcajada, P. Salcedo-Abraira, K. Kaneko, R. Kukobat, J. Kenvin, S. Keskin, S. Kitagawa, K. Otake, R. P. Lively, S. J. A DeWitt, P. L. Llewellyn, B. Lotsch, S. T. Emmerling, A. Pütz, C. Martí-Gastaldo, N. Muñoz, J. Garcia-Martinez, N. Linares, D. Maspoch, J. A. Suarez, P. Moghadam, R. Oktavian, R. Morris, P. Wheatley, J. Navarro, C. Petit, D. Danaci, M. Rosseinsky, A. Katsoulidis, M. Schroder, X. Han, S. Yang, C. Serre, G. Mouchaham, D. Sholl, R. Thyagarajan, D. Siderius, R. Q. Snurr, R. B. Goncalves, V. Ting, J. Rowlandson, T. Uemura, T. Iiyuka, M. van der Veen, D. Rega, V. Vanspeybroeck, A. Lamaire, S. Rogge, K. Walton, L. Bingel, S. Wuttke, J. Andreo, O. Yaghi, B. Zhang, C. Yavuz, T. Nguyen, F. Zamora, C. Montoro, H. Zhou, K. Angelo, D. Fairen-Jimenez, “How Reproducible Are Surface Areas Calculated from the BET Equation?”, Advanced Materials, 2022, 34, 2201502. https://doi.org/10.1002/adma.202201502

  31. K. Mukherjee, AW Dowling, Y. J. Colón*, “Sequential design of adsorption simulations in metal-organic frameworks.” Mol. Syst. Des. Eng., 2022, 7 (3), 248-259. https://doi.org/10.1039/D1ME00138H

  32. D. O. Abranches, Y. Zhang, E. J. Maginn, Y. J. Colón*, “Sigma profiles in deep learning: towards a universal molecular descriptor.” Chemical Communications, 2022, 58 (37), 5630-5633. https://doi.org/10.1039/D2CC01549H

  33. Z. Wang, @C. Villa Santos, A. Legrand, F. Haase, Y. Hará, K. Kanamori, T. Aoyama, K. Urayama, C. Doherty, G. J. Smales, B. R. Pauw, Y. J. Colón, S. Furukawa,” Multiscale structural control of linked metal-organic polyhedra by aging process.” Chem. Sci. 2021, 12, 12556-12563.

    https://doi.org/10.1039/D1SC02883A

  34. K. Mukherjee, Y. J. Colón*, “Machine learning and descriptor selection for the computational discovery of metal-organic frameworks.” Molecular Simulation 2022, 7, 248-259. https://doi.org/10.1080/08927022.2021.1916014

  35. R. A. Fritz, Y. J. Colón, F. Herrera, “Engineering entangled photon pairs with metal–organic frameworks.” Chemical Science 2021, 12 (10), 3475-3482. https://doi.org/10.1039/D0SC05572G

  36. R. Ma, Y. J. Colón*, T. Luo, “Transfer Learning Study of Gas Adsorption in Metal–Organic Frameworks.” ACS Applied Materials & Interfaces 2020. 12 (30), 34041-34048. *corresponding author https://doi.org/10.1021/acsami.0c06858

  37. Y. J. Colón*, S. Furukawa, “Understanding the role of linker flexibility in soft porous coordination polymers.” Mol. Syst. Des. Eng., 2020, 5, 284-293 *corresponding author https://doi.org/10.1039/C9ME00117D

  38. W. Chu, M. A. Webb, C. Deng, Y. J. Colón, Y. Kambe, S. Krishnan, P. F. Nealey, J. J. de Pablo, “Understanding Ion Mobility in P2VP/NMP+I- Polymer Electrolytes: A Combined Simulation and Experimental Study.” Macromolecules, 2020, 53 (8), 2783-2792. https://doi.org/10.1021/acs.macromol.9b02329

  39. A. Sturluson, M. T. Huynh, A. R. Kaija, C. Laird, S. Yoon, F. Hou, Z. Feng, C. E. Wilmer, Y. J. Colón*, Y. G. Chung, D. W. Siderius, C. M. Simon. “The role of molecular modelling and simulation in the discovery and deployment of metal-organic frameworks for gas storage and separation.” Mol. Sim., 2019, 45 (14-15), 1082-1121. *corresponding author https://doi.org/10.1080/08927022.2019.1648809

  40. Y. J. Colón, A. Z. Guo, L. W. Antony, K. Q. Hoffmann, and J. J. de Pablo, “Free energy of metal-organic framework self-assembly.” J. Chem. Phys. 2019, 150 (10), 104502. https://doi.org/10.1063/1.5063588

  41. Y. J. Colón, R. Q. Snurr, “The effect of co-adsorbed solvent molecules on H2 binding to metal alkoxides.” Phys. Chem. Chem. Phys. 2019, 21 (18), 9218-9224. https://doi.org/10.1039/C9CP00754G

  42. Q. Wu, D. Zhao, M. B. Goldey, A. Filatov, V. Sharapof, Y. J. Colón, Z. Cai, X. Jiang, J. Wang, W. Chen, J. J. de Pablo, G. Galli, and L. Yu, “Intra-molecular charge transfer and electron delocalization in non-fullerene organic solar cells.” ACS Applied Mater. Inter., 2018, 10 (12), 10043-10052. https://doi.org/10.1021/acsami.7b18717

  43. H. Sidky,* Y. J. Colón,* J. Helfferich, B. J. Sikora, C. Bezik, W. Chu, F. Giberti, A. Z. Guo, J. Lequieu, J. Li, J. Moller, M. Quevillon, M. Rahimi, H. Ramezani-Dakhel, V. Rathee, D. R. Reid, E. Sevgen, V. Thapar, M. Webb, X. Jiang, J. K. Whitmer, and J. J. de Pablo, “SSAGES: software suite for advanced general ensemble simulations.” J. Chem. Phys. 2018, 148(4), 044104. *co-first author https://doi.org/10.1063/1.5008853

  44. Y. J. Colón,* D. Gomez-Gualdron*, and R. Q. Snurr, “Topologically-guided automated construction of metal-organic frameworks and their evaluation for energy-related applications.” Cryst. Growth Des. 2017, 17, 5801-5810. *co-first author https://doi.org/10.1021/acs.cgd.7b00848

  45. D. Gomez-Gualdron*, Y. J. Colón,* X. Zhang, T. C. Wang, Y.-S. Chen, J. T. Hupp, T. Yildrim, O. K. Farha, J. Zhang, and R. Q. Snurr, “Evaluating topologically diverse metal-organic frameworks for cryo-adsorbed hydrogen storage.” Ener. Environ. Sci. 2016, 9, 3279-3289. *co-first author https://doi.org/10.1039/C6EE02104B

  46. B. J. Sikora, Y. J. Colón, R.Q. Snurr, “Continuous fractional component Monte Carlo simulations of high-density adsorption in metal-organic frameworks.” Mol. Simulat. 2015, 41, 1339-1347. https://doi.org/10.1080/08927022.2015.1043629

  47. S. Chakraborty, Y. J. Colón, R. Q. Snurr, S. Nguyen, “Hierarchically porous organic polymers: highly enhanced gas uptake and transport through templated synthesis.” Chem. Sci. 2015, 6, 384-389. https://doi.org/10.1039/C4SC02502D

  48. P. Ghosh, Y. J. Colón, R. Q. Snurr, “Water adsorption in UiO-66: the importance of defects.” Chem. Comm. 2014, 50, 11329-11331. https://doi.org/10.1039/C4CC04945D

  49. Y. J. Colón, R. Q. Snurr, “High-throughput computational screening of metal-organic frameworks” Chem. Soc. Rev. 2014, 43, 5735-5749. https://doi.org/10.1039/C4CS00070F

  50. Y. J. Colón,* D. Fairen-Jimenez,* C.E. Wilmer, R. Q. Snurr, “High-throughput screening of porous crystalline materials for hydrogen storage capacity near room temperature,” J. Phys. Chem. C. 2014, 118, 5383-5389.  *co-first author https://doi.org/10.1021/jp4122326

  51. Y. J. Colón, R. Krishna, R. Q. Snurr, “Strong influence of the H2 binding energy on Maxwell-Stefan diffusivity in NU-100, UiO-68, and IRMOF-16” Microporous Mesoporous Mater. 2014, 185, 190-196 https://doi.org/10.1016/j.micromeso.2013.10.031

  52. M. H. Weston, Y. J. Colón, Y.-S. Bae, S. J. Garibay, R. Q. Snurr, O. K. Farha, J. T. Hupp., S. Nguyen, “High propylene/propane adsorption selectivity in a copper (catecholate)-decorated porous organic polymer.” J. Mater. Chem. A, 2014, 2, 299-302. https://doi.org/10.1039/C3TA12999C

  53. Y. J. Colón, S. K. Brand, R.Q. Snurr, “Effect of metal alkoxide functionalization on hydrogen mobility in metal-organic frameworks.” Chem. Phys.  Lett. 2013, 577, 76-81 https://doi.org/10.1016/j.cplett.2013.05.021

  54. S. K. Brand,* Y. J. Colón,* R. B.  Getman, R. Q. Snurr, “Design strategies for metal alkoxide functionalized metal–organic frameworks for ambient temperature hydrogen storage.” Microporous Mesoporous Mater. 2013, 171, 103-109. *co-first author https://doi.org/10.1016/j.micromeso.2012.12.020

  55. M. J. Katz, Z. J. Brown, Y. J. Colón, P. W. Siu, K. A. Scheidt, R. Q. Snurr, J. T. Hupp, O. K. Farha, “A facile synthesis of UiO-66, UiO-67 and their derivatives.” Chem. Comm. 2013, 49, 9449-9451. https://doi.org/10.1039/C3CC46105J

  56. S. J. Garibay, M. H. Weston, J. E. Mondloch, Y. J. Colón, O. K. Farha, J. T. Hupp, S. T. Nguyen, “Accessing functionalized porous aromatic frameworks (PAFs) through a de novo approach.” Cryst. Eng. Comm. 2013, 15, 1515-1519. https://doi.org/10.1039/C2CE26595H

  57. Y. –S. Bae, B. G. Hauser, Y. J. Colón, J. T. Hupp, O. K. Farha, R. Q. Snurr, “High xenon/krypton selectivity in a metal-organic framework with small pores and strong adsorption sites.” Microporous Mesoporous Mater. 2013, 169, 176-179. https://doi.org/10.1016/j.micromeso.2012.11.013

  58. A. M. Pinto, H. Rodríguez, Y. J. Colón,  A. Arce, A. Soto, “Absorption of carbon dioxide in two binary mixtures of ionic liquids.” Ind. Eng. Chem. Res. 2013, 52, 5975-5984. https://doi.org/10.1021/ie303238h

  59. D. Fairen-Jimenez,* Y. J. Colón,* O.K. Farha, Y.-S. Bae, J. T. Hupp, R. Q. Snurr, “Understanding excess uptake maxima for hydrogen adsorption isotherms in frameworks with rht topology.” Chem. Comm. 2012, 48, 10496-10498. *co-first author https://doi.org/10.1039/C2CC35711A