Publications

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

  1. 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, just accepted

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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

  21. 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

  22. 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

  23. 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

  24. 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

  25. 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

  26. 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

  27. 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

  28. 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

  29. 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

  30. 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

  31. 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

  32. 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

  33. 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

  34. 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

  35. 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

  36. 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

  37. 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

  38. 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

  39. 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

  40. 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

  41. 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

  42. 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

  43. 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

  44. 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

  45. 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

  46. 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

  47. 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

  48. 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

  49. 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

  50. 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

  51. 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

  52. 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