Exploring the Structural, Dynamic, and Functional Properties of Metal–Organic Frameworks through Molecular Modeling

Formalik, Filip; Shi, Kaihang; Joodaki, Faramarz; Wang, Xijun; Snurr, Randall Q.

doi:10.1002/adfm.202308130

Exploring the Structural, Dynamic, and Functional Properties of Metal–Organic Frameworks through Molecular Modeling

Journal Article · Tue Oct 17 00:00:00 EDT 2023 · Advanced Functional Materials

DOI:https://doi.org/10.1002/adfm.202308130· OSTI ID:2510792

Formalik, Filip ^[1]; Shi, Kaihang ^[2]; Joodaki, Faramarz ^[3]; Wang, Xijun ^[3]; ^[3]

Northwestern University, Evanston, IL (United States); Wroclaw University of Science and Technology (Poland)
Northwestern University, Evanston, IL (United States); University at Buffalo, The State University of New York, NY (United States)
Northwestern University, Evanston, IL (United States)

This review spotlights the role of atomic-level modeling in research on metal-organic frameworks (MOFs), especially the key methodologies of density functional theory (DFT), Monte Carlo (MC) simulations, and molecular dynamics (MD) simulations. The discussion focuses on how periodic and cluster-based DFT calculations can provide novel insights into MOF properties, with a focus on predicting structural transformations, understanding thermodynamic properties and catalysis, and providing information or properties that are fed into classical simulations such as force field parameters or partial charges. Classical simulation methods, highlighting force field selection, databases of MOFs for high-throughput screening, and the synergistic nature of MC and MD simulations, are described. By predicting equilibrium thermodynamic and dynamic properties, these methods offer a wide perspective on MOF behavior and mechanisms. Additionally, the incorporation of machine learning (ML) techniques into quantum and classical simulations is discussed. These methods can enhance accuracy, expedite simulation setup, reduce computational costs, as well as predict key parameters, optimize geometries, and estimate MOF stability. By charting the growth and promise of computational research in the MOF field, the aim is to provide insights and recommendations to facilitate the incorporation of computational modeling more broadly into MOF research.

View Accepted Manuscript (DOE)

Research Organization:: University of Minnesota, Minneapolis, MN (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES); U.S. National Science Foundation (NSF)

Grant/Contract Number:: SC0023454

OSTI ID:: 2510792

Journal Information:: Advanced Functional Materials, Journal Name: Advanced Functional Materials Journal Issue: 43 Vol. 34; ISSN 1616-301X

Publisher:: WileyCopyright Statement

Country of Publication:: United States

Language:: English

References (238)

Density Functional Theory Sholl, David S.; Steckel, Janice A. Wiley https://doi.org/10.1002/9780470447710	book	March 2009
Modeling Gas Adsorption in Flexible Metal–Organic Frameworks via Hybrid Monte Carlo/Molecular Dynamics Schemes Rogge, Sven M. J.; Goeminne, Ruben; Demuynck, Ruben Advanced Theory and Simulations, Vol. 2, Issue 4 https://doi.org/10.1002/adts.201800177	journal	January 2019
Design, Parameterization, and Implementation of Atomic Force Fields for Adsorption in Nanoporous Materials Dubbeldam, David; Walton, Krista S.; Vlugt, Thijs J. H. Advanced Theory and Simulations, Vol. 2, Issue 11 https://doi.org/10.1002/adts.201900135	journal	September 2019
Zirconium-Metalloporphyrin PCN-222: Mesoporous Metal-Organic Frameworks with Ultrahigh Stability as Biomimetic Catalysts Feng, Dawei; Gu, Zhi-Yuan; Li, Jian-Rong Angewandte Chemie, Vol. 124, Issue 41, p. 10453-10456 https://doi.org/10.1002/ange.201204475	journal	August 2012
Three-Dimensional Framework with Channeling Cavities for Small Molecules:{[M2(4, 4′-bpy)3(NO3)4]·xH2O}n(M Co, Ni, Zn) Kondo, Mitsuru; Yoshitomi, Tomomichi; Matsuzaka, Hiroyuki Angewandte Chemie International Edition in English, Vol. 36, Issue 16 https://doi.org/10.1002/anie.199717251	journal	September 1997
Ligand-Directed Strategy for Zeolite-Type Metal–Organic Frameworks: Zinc(II) Imidazolates with Unusual Zeolitic Topologies Huang, Xiao-Chun; Lin, Yan-Yong; Zhang, Jie-Peng Angewandte Chemie International Edition, Vol. 45, Issue 10, p. 1557-1559 https://doi.org/10.1002/anie.200503778	journal	February 2006
Molecular Dynamics Simulations of Breathing MOFs: Structural Transformations of MIL-53(Cr) upon Thermal Activation and CO ₂ Adsorption Salles, Fabrice; Ghoufi, Aziz; Maurin, Guillaume Angewandte Chemie International Edition, Vol. 47, Issue 44 https://doi.org/10.1002/anie.200803067	journal	October 2008
The Effect of Pressure on ZIF-8: Increasing Pore Size with Pressure and the Formation of a High-Pressure Phase at 1.47 GPa Moggach, Stephen A.; Bennett, Thomas D.; Cheetham, Anthony K. Angewandte Chemie International Edition, Vol. 48, Issue 38 https://doi.org/10.1002/anie.200902643	journal	September 2009
Balancing Mechanical Stability and Ultrahigh Porosity in Crystalline Framework Materials Hönicke, Ines M.; Senkovska, Irena; Bon, Volodymyr Angewandte Chemie International Edition, Vol. 57, Issue 42 https://doi.org/10.1002/anie.201808240	journal	October 2018
Collective Breathing in an Eightfold Interpenetrated Metal–Organic Framework: From Mechanistic Understanding towards Threshold Sensing Architectures Roztocki, Kornel; Formalik, Filip; Krawczuk, Anna Angewandte Chemie International Edition, Vol. 59, Issue 11 https://doi.org/10.1002/anie.201914198	journal	January 2020
Best‐Practice DFT Protocols for Basic Molecular Computational Chemistry** Bursch, Markus; Mewes, Jan‐Michael; Hansen, Andreas Angewandte Chemie International Edition, Vol. 61, Issue 42 https://doi.org/10.1002/anie.202205735	journal	September 2022
A Rationale for the Large Breathing of the Porous Aluminum Terephthalate (MIL-53) Upon Hydration Loiseau, Thierry; Serre, Christian; Huguenard, Clarisse Chemistry - A European Journal, Vol. 10, Issue 6 https://doi.org/10.1002/chem.200305413	journal	March 2004
Supramolecular Binding Thermodynamics by Dispersion-Corrected Density Functional Theory Grimme, Stefan Chemistry - A European Journal, Vol. 18, Issue 32 https://doi.org/10.1002/chem.201200497	journal	July 2012
Semiempirical GGA-type density functional constructed with a long-range dispersion correction Grimme, Stefan Journal of Computational Chemistry, Vol. 27, Issue 15, p. 1787-1799 https://doi.org/10.1002/jcc.20495	journal	January 2006
Effect of the damping function in dispersion corrected density functional theory Grimme, Stefan; Ehrlich, Stephan; Goerigk, Lars Journal of Computational Chemistry, Vol. 32, Issue 7 https://doi.org/10.1002/jcc.21759	journal	March 2011
QuickFF: A program for a quick and easy derivation of force fields for metal-organic frameworks from ab initio input Vanduyfhuys, Louis; Vandenbrande, Steven; Verstraelen, Toon Journal of Computational Chemistry, Vol. 36, Issue 13 https://doi.org/10.1002/jcc.23877	journal	March 2015
Cassandra: An open source Monte Carlo package for molecular simulation Shah, Jindal K.; Marin-Rimoldi, Eliseo; Mullen, Ryan Gotchy Journal of Computational Chemistry, Vol. 38, Issue 19 https://doi.org/10.1002/jcc.24807	journal	April 2017
Extension of the QuickFF force field protocol for an improved accuracy of structural, vibrational, mechanical and thermal properties of metal-organic frameworks Vanduyfhuys, Louis; Vandenbrande, Steven; Wieme, Jelle Journal of Computational Chemistry, Vol. 39, Issue 16 https://doi.org/10.1002/jcc.25173	journal	February 2018
Optimization of equilibrium geometries and transition structures Schlegel, H. Bernhard Journal of Computational Chemistry, Vol. 3, Issue 2 https://doi.org/10.1002/jcc.540030212	journal	July 1982
Ab initio study of solvated molecules: a new implementation of the polarizable continuum model Cossi, Maurizio; Barone, Vincenzo; Cammi, Roberto Chemical Physics Letters, Vol. 255, Issue 4-6 https://doi.org/10.1016/0009-2614(96)00349-1	journal	June 1996
Theoretical studies of spin arrangement of adsorbed organic radicals in metal-organic nanoporous cavity Kawakami, Takashi; Takamizawa, Satoshi; Kitagawa, Yasutaka Polyhedron, Vol. 20, Issue 11-14 https://doi.org/10.1016/S0277-5387(01)00594-0	journal	May 2001
Origins of Negative Gas Adsorption Evans, Jack D.; Bocquet, Lydéric; Coudert, François-Xavier Chem, Vol. 1, Issue 6 https://doi.org/10.1016/j.chempr.2016.11.004	journal	December 2016
HOOMD-blue: A Python package for high-performance molecular dynamics and hard particle Monte Carlo simulations Anderson, Joshua A.; Glaser, Jens; Glotzer, Sharon C. Computational Materials Science, Vol. 173 https://doi.org/10.1016/j.commatsci.2019.109363	journal	February 2020
LAMMPS - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales Thompson, Aidan P.; Aktulga, H. Metin; Berger, Richard Computer Physics Communications, Vol. 271 https://doi.org/10.1016/j.cpc.2021.108171	journal	February 2022
Thermal conductivity of metal-organic framework 5 (MOF-5): Part I. Molecular dynamics simulations Huang, B. L.; McGaughey, A. J. H.; Kaviany, M. International Journal of Heat and Mass Transfer, Vol. 50, Issue 3-4, p. 393-404 https://doi.org/10.1016/j.ijheatmasstransfer.2006.10.002	journal	February 2007
Pore opening and breathing transitions in metal-organic frameworks: Coupling adsorption and deformation Formalik, Filip; Neimark, Alexander V.; Rogacka, Justyna Journal of Colloid and Interface Science, Vol. 578 https://doi.org/10.1016/j.jcis.2020.05.105	journal	October 2020
Structure-Mechanical Stability Relations of Metal-Organic Frameworks via Machine Learning Moghadam, Peyman Z.; Rogge, Sven M. J.; Li, Aurelia Matter, Vol. 1, Issue 1 https://doi.org/10.1016/j.matt.2019.03.002	journal	July 2019
Machine learning the quantum-chemical properties of metal–organic frameworks for accelerated materials discovery Rosen, Andrew S.; Iyer, Shaelyn M.; Ray, Debmalya Matter, Vol. 4, Issue 5 https://doi.org/10.1016/j.matt.2021.02.015	journal	May 2021
Absorbing stress via molecular crumple zones: Strain engineering flexibility into the rigid UiO-66 material Rogge, Sven M. J.; Borgmans, Sander; Van Speybroeck, Veronique Matter, Vol. 6, Issue 5 https://doi.org/10.1016/j.matt.2023.02.009	journal	May 2023
A database of ultrastable MOFs reassembled from stable fragments with machine learning models Nandy, Aditya; Yue, Shuwen; Oh, Changhwan Matter, Vol. 6, Issue 5 https://doi.org/10.1016/j.matt.2023.03.009	journal	May 2023
Recent advances in gas storage and separation using metal–organic frameworks Li, Hao; Wang, Kecheng; Sun, Yujia Materials Today, Vol. 21, Issue 2 https://doi.org/10.1016/j.mattod.2017.07.006	journal	March 2018
Effect of low frequency phonons on structural properties of ZIFs with SOD topology Formalik, Filip; Fischer, Michael; Rogacka, Justyna Microporous and Mesoporous Materials, Vol. 304 https://doi.org/10.1016/j.micromeso.2018.09.033	journal	September 2020
GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers Abraham, Mark James; Murtola, Teemu; Schulz, Roland SoftwareX, Vol. 1-2 https://doi.org/10.1016/j.softx.2015.06.001	journal	September 2015
GOMC: GPU Optimized Monte Carlo for the simulation of phase equilibria and physical properties of complex fluids Nejahi, Younes; Soroush Barhaghi, Mohammad; Mick, Jason SoftwareX, Vol. 9 https://doi.org/10.1016/j.softx.2018.11.005	journal	January 2019
Topologically Guided, Automated Construction of Metal–Organic Frameworks and Their Evaluation for Energy-Related Applications Colón, Yamil J.; Gómez-Gualdrón, Diego A.; Snurr, Randall Q. Crystal Growth & Design, Vol. 17, Issue 11 https://doi.org/10.1021/acs.cgd.7b00848	journal	September 2017
ARC–MOF: A Diverse Database of Metal-Organic Frameworks with DFT-Derived Partial Atomic Charges and Descriptors for Machine Learning Burner, Jake; Luo, Jun; White, Andrew Chemistry of Materials, Vol. 35, Issue 3 https://doi.org/10.1021/acs.chemmater.2c02485	journal	January 2023
Development of a Cambridge Structural Database Subset: A Collection of Metal–Organic Frameworks for Past, Present, and Future Moghadam, Peyman Z.; Li, Aurelia; Wiggin, Seth B. Chemistry of Materials, Vol. 29, Issue 7 https://doi.org/10.1021/acs.chemmater.7b00441	journal	March 2017
Graph Networks as a Universal Machine Learning Framework for Molecules and Crystals Chen, Chi; Ye, Weike; Zuo, Yunxing Chemistry of Materials, Vol. 31, Issue 9 https://doi.org/10.1021/acs.chemmater.9b01294	journal	April 2019
Role of Structural Defects in the Adsorption and Separation of C3 Hydrocarbons in Zr-Fumarate-MOF (MOF-801) Iacomi, Paul; Formalik, Filip; Marreiros, Joao Chemistry of Materials, Vol. 31, Issue 20 https://doi.org/10.1021/acs.chemmater.9b02322	journal	September 2019
Big-Data Science in Porous Materials: Materials Genomics and Machine Learning Jablonka, Kevin Maik; Ongari, Daniele; Moosavi, Seyed Mohamad Chemical Reviews, Vol. 120, Issue 16 https://doi.org/10.1021/acs.chemrev.0c00004	journal	June 2020
Conceptual and Practical Aspects of Metal–Organic Frameworks for Solid–Gas Reactions Iliescu, Andrei; Oppenheim, Julius J.; Sun, Chenyue Chemical Reviews, Vol. 123, Issue 9 https://doi.org/10.1021/acs.chemrev.2c00537	journal	February 2023
Brønsted Acidity in Metal–Organic Frameworks Jiang, Juncong; Yaghi, Omar M. Chemical Reviews, Vol. 115, Issue 14 https://doi.org/10.1021/acs.chemrev.5b00221	journal	June 2015
Metal–Organic Frameworks in Heterogeneous Catalysis: Recent Progress, New Trends, and Future Perspectives Bavykina, Anastasiya; Kolobov, Nikita; Khan, Il Son Chemical Reviews, Vol. 120, Issue 16 https://doi.org/10.1021/acs.chemrev.9b00685	journal	March 2020
Computational Screening of Bimetal-Functionalized Zr ₆ O ₈ MOF Nodes for Methane C–H Bond Activation Pahls, Dale R.; Ortuño, Manuel A.; Winegar, Peter H. Inorganic Chemistry, Vol. 56, Issue 15 https://doi.org/10.1021/acs.inorgchem.7b01334	journal	July 2017
MOFX-DB: An Online Database of Computational Adsorption Data for Nanoporous Materials Bobbitt, N. Scott; Shi, Kaihang; Bucior, Benjamin J. Journal of Chemical & Engineering Data, Vol. 68, Issue 2 https://doi.org/10.1021/acs.jced.2c00583	journal	January 2023
Advances, Updates, and Analytics for the Computation-Ready, Experimental Metal–Organic Framework Database: CoRE MOF 2019 Chung, Yongchul G.; Haldoupis, Emmanuel; Bucior, Benjamin J. Journal of Chemical & Engineering Data, Vol. 64, Issue 12 https://doi.org/10.1021/acs.jced.9b00835	journal	November 2019
Fast and Accurate Machine Learning Strategy for Calculating Partial Atomic Charges in Metal–Organic Frameworks Kancharlapalli, Srinivasu; Gopalan, Arun; Haranczyk, Maciej Journal of Chemical Theory and Computation, Vol. 17, Issue 5 https://doi.org/10.1021/acs.jctc.0c01229	journal	March 2021
Combined Deep Learning and Classical Potential Approach for Modeling Diffusion in UiO-66 Achar, Siddarth K.; Wardzala, Jacob J.; Bernasconi, Leonardo Journal of Chemical Theory and Computation, Vol. 18, Issue 6 https://doi.org/10.1021/acs.jctc.2c00010	journal	June 2022
Effects of Degrees of Freedom on Calculating Diffusion Properties in Nanoporous Materials Xu, Henglu; Cabriolu, Raffaela; Smit, Berend Journal of Chemical Theory and Computation, Vol. 18, Issue 5 https://doi.org/10.1021/acs.jctc.2c00094	journal	April 2022
Machine Learning Models Predict Calculation Outcomes with the Transferability Necessary for Computational Catalysis Duan, Chenru; Nandy, Aditya; Adamji, Husain Journal of Chemical Theory and Computation, Vol. 18, Issue 7 https://doi.org/10.1021/acs.jctc.2c00331	journal	June 2022
Minimal Basis Iterative Stockholder: Atoms in Molecules for Force-Field Development Verstraelen, Toon; Vandenbrande, Steven; Heidar-Zadeh, Farnaz Journal of Chemical Theory and Computation, Vol. 12, Issue 8 https://doi.org/10.1021/acs.jctc.6b00456	journal	July 2016
Extension of the Universal Force Field for Metal–Organic Frameworks Coupry, Damien E.; Addicoat, Matthew A.; Heine, Thomas Journal of Chemical Theory and Computation, Vol. 12, Issue 10 https://doi.org/10.1021/acs.jctc.6b00664	journal	September 2016
Where Does the Density Localize? Convergent Behavior for Global Hybrids, Range Separation, and DFT+U Gani, Terry Z. H.; Kulik, Heather J. Journal of Chemical Theory and Computation, Vol. 12, Issue 12 https://doi.org/10.1021/acs.jctc.6b00937	journal	November 2016
The Monomer Electron Density Force Field (MEDFF): A Physically Inspired Model for Noncovalent Interactions Vandenbrande, Steven; Waroquier, Michel; Speybroeck, Veronique Van Journal of Chemical Theory and Computation, Vol. 13, Issue 1 https://doi.org/10.1021/acs.jctc.6b00969	journal	December 2016
Evaluating Charge Equilibration Methods To Generate Electrostatic Fields in Nanoporous Materials Ongari, Daniele; Boyd, Peter G.; Kadioglu, Ozge Journal of Chemical Theory and Computation, Vol. 15, Issue 1 https://doi.org/10.1021/acs.jctc.8b00669	journal	November 2018
Applicability of Tail Corrections in the Molecular Simulations of Porous Materials Jablonka, Kevin Maik; Ongari, Daniele; Smit, Berend Journal of Chemical Theory and Computation, Vol. 15, Issue 10 https://doi.org/10.1021/acs.jctc.9b00586	journal	August 2019
Seeing Is Believing: Experimental Spin States from Machine Learning Model Structure Predictions Taylor, Michael G.; Yang, Tzuhsiung; Lin, Sean The Journal of Physical Chemistry A, Vol. 124, Issue 16 https://doi.org/10.1021/acs.jpca.0c01458	journal	March 2020
Machine Learning Interatomic Potentials and Long-Range Physics Anstine, Dylan M.; Isayev, Olexandr The Journal of Physical Chemistry A, Vol. 127, Issue 11 https://doi.org/10.1021/acs.jpca.2c06778	journal	February 2023
Importance of Lattice Constants in QM/MM Calculations on Metal–Organic Frameworks Yang, Bo; Wu, Xin-Ping; Gagliardi, Laura The Journal of Physical Chemistry B, Vol. 125, Issue 22 https://doi.org/10.1021/acs.jpcb.1c02328	journal	May 2021
Efficient and Accurate Charge Assignments via a Multilayer Connectivity-Based Atom Contribution (m-CBAC) Approach Zou, Changlong; Penley, Drace R.; Cho, Eun Hyun The Journal of Physical Chemistry C, Vol. 124, Issue 21 https://doi.org/10.1021/acs.jpcc.0c01524	journal	April 2020
Effect of Flexibility on Thermal Transport in Breathing Porous Crystals Sezginel, Kutay B.; Lee, Sangsuk; Babaei, Hasan The Journal of Physical Chemistry C, Vol. 124, Issue 34 https://doi.org/10.1021/acs.jpcc.0c04353	journal	July 2020
Message Passing Neural Networks for Partial Charge Assignment to Metal–Organic Frameworks Raza, Ali; Sturluson, Arni; Simon, Cory M. The Journal of Physical Chemistry C, Vol. 124, Issue 35 https://doi.org/10.1021/acs.jpcc.0c04903	journal	August 2020
Phonons and Adsorption-Induced Deformations in ZIFs: Is It Really a Gate Opening? Formalik, Filip; Mazur, Bartosz; Fischer, Michael The Journal of Physical Chemistry C, Vol. 125, Issue 14 https://doi.org/10.1021/acs.jpcc.1c01342	journal	April 2021
Molecular Simulation Studies of the Diffusion of Methane, Ethane, Propane, and Propylene in ZIF-8 Krokidas, Panagiotis; Castier, Marcelo; Moncho, Salvador The Journal of Physical Chemistry C, Vol. 119, Issue 48 https://doi.org/10.1021/acs.jpcc.5b08554	journal	November 2015
ZIF-67 Framework: A Promising New Candidate for Propylene/Propane Separation. Experimental Data and Molecular Simulations Krokidas, Panagiotis; Castier, Marcelo; Moncho, Salvador The Journal of Physical Chemistry C, Vol. 120, Issue 15 https://doi.org/10.1021/acs.jpcc.6b00305	journal	April 2016
Accelerated Computational Analysis of Metal–Organic Frameworks for Oxidation Catalysis Vogiatzis, Konstantinos D.; Haldoupis, Emmanuel; Xiao, Dianne J. The Journal of Physical Chemistry C, Vol. 120, Issue 33 https://doi.org/10.1021/acs.jpcc.6b07115	journal	August 2016
Thermodynamics of the Flexible Metal–Organic Framework Material MIL-53(Cr) From First-Principles Cockayne, Eric The Journal of Physical Chemistry C, Vol. 121, Issue 8 https://doi.org/10.1021/acs.jpcc.6b11692	journal	February 2017
Computational Study of ZIF-8 and ZIF-67 Performance for Separation of Gas Mixtures Krokidas, Panagiotis; Castier, Marcelo; Economou, Ioannis G. The Journal of Physical Chemistry C, Vol. 121, Issue 33 https://doi.org/10.1021/acs.jpcc.7b05700	journal	August 2017
Methane Adsorption in Zr-Based MOFs: Comparison and Critical Evaluation of Force Fields Vandenbrande, Steven; Verstraelen, Toon; Gutiérrez-Sevillano, Juan José The Journal of Physical Chemistry C, Vol. 121, Issue 45 https://doi.org/10.1021/acs.jpcc.7b08971	journal	November 2017
Elucidating the Vibrational Fingerprint of the Flexible Metal–Organic Framework MIL-53(Al) Using a Combined Experimental/Computational Approach Hoffman, Alexander E. J.; Vanduyfhuys, Louis; Nevjestić, Irena The Journal of Physical Chemistry C, Vol. 122, Issue 5 https://doi.org/10.1021/acs.jpcc.7b11031	journal	January 2018
Insights into Catalytic Hydrolysis of Organophosphate Warfare Agents by Metal–Organic Framework NU-1000 Chen, Haoyuan; Liao, Peilin; Mendonca, Matthew L. The Journal of Physical Chemistry C, Vol. 122, Issue 23 https://doi.org/10.1021/acs.jpcc.8b03641	journal	May 2018
Probing the Mechanochemistry of Metal–Organic Frameworks with Low-Frequency Vibrational Spectroscopy Zhang, Wei; Maul, Jefferson; Vulpe, Diana The Journal of Physical Chemistry C, Vol. 122, Issue 48 https://doi.org/10.1021/acs.jpcc.8b08334	journal	November 2018
Molecular-Level Insight into CO ₂ Adsorption on the Zirconium-Based Metal–Organic Framework, UiO-66: A Combined Spectroscopic and Computational Approach Grissom, Tyler G.; Driscoll, Darren M.; Troya, Diego The Journal of Physical Chemistry C, Vol. 123, Issue 22 https://doi.org/10.1021/acs.jpcc.9b02513	journal	May 2019
Efficient Generation of Large Collections of Metal–Organic Framework Structures Containing Well-Defined Point Defects Yu, Zhenzi; Jamdade, Shubham; Yu, Xiaohan The Journal of Physical Chemistry Letters, Vol. 14, Issue 29 https://doi.org/10.1021/acs.jpclett.3c01524	journal	July 2023
High-Throughput Computational Screening of Multivariate Metal–Organic Frameworks (MTV-MOFs) for CO ₂ Capture Li, Song; Chung, Yongchul G.; Simon, Cory M. The Journal of Physical Chemistry Letters, Vol. 8, Issue 24 https://doi.org/10.1021/acs.jpclett.7b02700	journal	December 2017
Defining New Limits in Gas Separations Using Modified ZIF Systems Krokidas, Panagiotis; Moncho, Salvador; Brothers, Edward N. ACS Applied Materials & Interfaces, Vol. 12, Issue 18 https://doi.org/10.1021/acsami.0c02886	journal	April 2020
Exploring the Tunability of Trimetallic MOF Nodes for Partial Oxidation of Methane to Methanol Barona, Melissa; Snurr, Randall Q. ACS Applied Materials & Interfaces, Vol. 12, Issue 25 https://doi.org/10.1021/acsami.0c06241	journal	May 2020
Topology-Dependent Alkane Diffusion in Zirconium Metal–Organic Frameworks Bukowski, Brandon C.; Snurr, Randall Q. ACS Applied Materials & Interfaces, Vol. 12, Issue 50 https://doi.org/10.1021/acsami.0c17797	journal	December 2020
Computational Screening of Trillions of Metal–Organic Frameworks for High-Performance Methane Storage Lee, Sangwon; Kim, Baekjun; Cho, Hyun ACS Applied Materials & Interfaces, Vol. 13, Issue 20 https://doi.org/10.1021/acsami.1c02471	journal	May 2021
Diversifying Databases of Metal Organic Frameworks for High-Throughput Computational Screening Majumdar, Sauradeep; Moosavi, Seyed Mohamad; Jablonka, Kevin Maik ACS Applied Materials & Interfaces, Vol. 13, Issue 51 https://doi.org/10.1021/acsami.1c16220	journal	December 2021
Insights and Heuristics for Predicting Diffusion Rates of Chemical Warfare Agents in Zirconium Metal–Organic Frameworks Bukowski, Brandon C.; Snurr, Randall Q. ACS Applied Materials & Interfaces, Vol. 14, Issue 50 https://doi.org/10.1021/acsami.2c17313	journal	December 2022
Influence of First and Second Coordination Environment on Structural Fe(II) Sites in MIL-101 for C–H Bond Activation in Methane Vitillo, Jenny G.; Lu, Connie C.; Cramer, Christopher J. ACS Catalysis, Vol. 11, Issue 2 https://doi.org/10.1021/acscatal.0c03906	journal	December 2020
Using Computational Chemistry To Reveal Nature’s Blueprints for Single-Site Catalysis of C–H Activation Nandy, Aditya; Adamji, Husain; Kastner, David W. ACS Catalysis, Vol. 12, Issue 15 https://doi.org/10.1021/acscatal.2c02096	journal	July 2022
Quantum Chemical Characterization of Structural Single Fe(II) Sites in MIL-Type Metal–Organic Frameworks for the Oxidation of Methane to Methanol and Ethane to Ethanol Vitillo, Jenny G.; Bhan, Aditya; Cramer, Christopher J. ACS Catalysis, Vol. 9, Issue 4 https://doi.org/10.1021/acscatal.8b04813	journal	January 2019
Structure–Activity Relationships That Identify Metal–Organic Framework Catalysts for Methane Activation Rosen, Andrew S.; Notestein, Justin M.; Snurr, Randall Q. ACS Catalysis, Vol. 9, Issue 4 https://doi.org/10.1021/acscatal.8b05178	journal	March 2019
Computational Predictions and Experimental Validation of Alkane Oxidative Dehydrogenation by Fe ₂ M MOF Nodes Barona, Melissa; Ahn, Sol; Morris, William ACS Catalysis, Vol. 10, Issue 2 https://doi.org/10.1021/acscatal.9b03932	journal	December 2019
MOF Linker Extension Strategy for Enhanced Atmospheric Water Harvesting Hanikel, Nikita; Kurandina, Daria; Chheda, Saumil ACS Central Science, Vol. 9, Issue 3 https://doi.org/10.1021/acscentsci.3c00018	journal	March 2023
In Silico Tuning of the Pore Surface Functionality in Al-MOFs for Trace CH₃I Capture Wu, Xiaoyu; Chen, Linjiang; Amigues, Eric Jean ACS Omega, Vol. 6, Issue 28 https://doi.org/10.1021/acsomega.1c02072	journal	July 2021
Computation-Ready, Experimental Metal–Organic Frameworks: A Tool To Enable High-Throughput Screening of Nanoporous Crystals Chung, Yongchul G.; Camp, Jeffrey; Haranczyk, Maciej Chemistry of Materials, Vol. 26, Issue 21 https://doi.org/10.1021/cm502594j	journal	October 2014
Metal–Organic Frameworks for Separations Li, Jian-Rong; Sculley, Julian; Zhou, Hong-Cai Chemical Reviews, Vol. 112, Issue 2, p. 869-932 https://doi.org/10.1021/cr200190s	journal	September 2011
Hydrogen Storage in Metal–Organic Frameworks Suh, Myunghyun Paik; Park, Hye Jeong; Prasad, Thazhe Kootteri Chemical Reviews, Vol. 112, Issue 2, p. 782-835 https://doi.org/10.1021/cr200274s	journal	September 2011
Carbon Dioxide Capture in Metal–Organic Frameworks Sumida, Kenji; Rogow, David L.; Mason, Jarad A. Chemical Reviews, Vol. 112, Issue 2, p. 724-781 https://doi.org/10.1021/cr2003272	journal	September 2011
Engineering Metal Organic Frameworks for Heterogeneous Catalysis Corma, A.; García, H.; Llabrés i Xamena, F. X. Chemical Reviews, Vol. 110, Issue 8, p. 4606-4655 https://doi.org/10.1021/cr9003924	journal	August 2010
Chemically Meaningful Atomic Charges That Reproduce the Electrostatic Potential in Periodic and Nonperiodic Materials Manz, Thomas A.; Sholl, David S. Journal of Chemical Theory and Computation, Vol. 6, Issue 8 https://doi.org/10.1021/ct100125x	journal	July 2010
Computational Thermochemistry: Scale Factor Databases and Scale Factors for Vibrational Frequencies Obtained from Electronic Model Chemistries Alecu, I. M.; Zheng, Jingjing; Zhao, Yan Journal of Chemical Theory and Computation, Vol. 6, Issue 9 https://doi.org/10.1021/ct100326h	journal	August 2010
Extension of the Universal Force Field to Metal–Organic Frameworks Addicoat, Matthew A.; Vankova, Nina; Akter, Ismot Farjana Journal of Chemical Theory and Computation, Vol. 10, Issue 2 https://doi.org/10.1021/ct400952t	journal	January 2014
Force-Field Development from Electronic Structure Calculations with Periodic Boundary Conditions: Applications to Gaseous Adsorption and Transport in Metal–Organic Frameworks Lin, Li-Chiang; Lee, Kyuho; Gagliardi, Laura Journal of Chemical Theory and Computation, Vol. 10, Issue 4 https://doi.org/10.1021/ct500094w	journal	March 2014
Electrostatic Potential Derived Atomic Charges for Periodic Systems Using a Modified Error Functional Campañá, Carlos; Mussard, Bastien; Woo, Tom K. Journal of Chemical Theory and Computation, Vol. 5, Issue 10 https://doi.org/10.1021/ct9003405	journal	August 2009
A New Two-Constant Equation of State Peng, Ding-Yu; Robinson, Donald B. Industrial & Engineering Chemistry Fundamentals, Vol. 15, Issue 1 https://doi.org/10.1021/i160057a011	journal	February 1976
Charge equilibration for molecular dynamics simulations Rappe, Anthony K.; Goddard, William A. The Journal of Physical Chemistry, Vol. 95, Issue 8 https://doi.org/10.1021/j100161a070	journal	April 1991
DREIDING: a generic force field for molecular simulations Mayo, Stephen L.; Olafson, Barry D.; Goddard, William A. The Journal of Physical Chemistry, Vol. 94, Issue 26, p. 8897-8909 https://doi.org/10.1021/j100389a010	journal	December 1990
UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations Rappe, A. K.; Casewit, C. J.; Colwell, K. S. Journal of the American Chemical Society, Vol. 114, Issue 25, p. 10024-10035 https://doi.org/10.1021/ja00051a040	journal	December 1992
Hydrothermal Synthesis of a Metal-Organic Framework Containing Large Rectangular Channels Yaghi, O. M.; Li, Hailian Journal of the American Chemical Society, Vol. 117, Issue 41, p. 10401-10402 https://doi.org/10.1021/ja00146a033	journal	October 1995
Infinite polymeric frameworks consisting of three dimensionally linked rod-like segments Hoskins, Bernard F.; Robson, Richard Journal of the American Chemical Society, Vol. 111, Issue 15 https://doi.org/10.1021/ja00197a079	journal	July 1989
Rod Packings and Metal−Organic Frameworks Constructed from Rod-Shaped Secondary Building Units Rosi, Nathaniel L.; Kim, Jaheon; Eddaoudi, Mohamed Journal of the American Chemical Society, Vol. 127, Issue 5, p. 1504-1518 https://doi.org/10.1021/ja045123o	journal	February 2005
Applicability of the BET Method for Determining Surface Areas of Microporous Metal−Organic Frameworks Walton, Krista S.; Snurr, Randall Q. Journal of the American Chemical Society, Vol. 129, Issue 27 https://doi.org/10.1021/ja071174k	journal	July 2007
Opening the Gate: Framework Flexibility in ZIF-8 Explored by Experiments and Simulations Fairen-Jimenez, D.; Moggach, S. A.; Wharmby, M. T. Journal of the American Chemical Society, Vol. 133, Issue 23 https://doi.org/10.1021/ja202154j	journal	June 2011
Metal–Organic Framework Materials with Ultrahigh Surface Areas: Is the Sky the Limit? Farha, Omar K.; Eryazici, Ibrahim; Jeong, Nak Cheon Journal of the American Chemical Society, Vol. 134, Issue 36, p. 15016-15021 https://doi.org/10.1021/ja3055639	journal	August 2012
Vapor-Phase Metalation by Atomic Layer Deposition in a Metal–Organic Framework Mondloch, Joseph E.; Bury, Wojciech; Fairen-Jimenez, David Journal of the American Chemical Society, Vol. 135, Issue 28, p. 10294-10297 https://doi.org/10.1021/ja4050828	journal	May 2013
Water Adsorption in Porous Metal–Organic Frameworks and Related Materials Furukawa, Hiroyasu; Gándara, Felipe; Zhang, Yue-Biao Journal of the American Chemical Society, Vol. 136, Issue 11, p. 4369-4381 https://doi.org/10.1021/ja500330a	journal	March 2014
Reversible Structural Transition in MIL-53 with Large Temperature Hysteresis Liu, Yun; Her, Jae-Hyuk; Dailly, Anne Journal of the American Chemical Society, Vol. 130, Issue 35 https://doi.org/10.1021/ja803669w	journal	September 2008
A New Zirconium Inorganic Building Brick Forming Metal Organic Frameworks with Exceptional Stability Cavka, Jasmina Hafizovic; Jakobsen, Søren; Olsbye, Unni Journal of the American Chemical Society, Vol. 130, Issue 42, p. 13850-13851 https://doi.org/10.1021/ja8057953	journal	October 2008
Node-Accessible Zirconium MOFs Lu, Zhiyong; Liu, Jian; Zhang, Xuan Journal of the American Chemical Society, Vol. 142, Issue 50 https://doi.org/10.1021/jacs.0c09782	journal	December 2020
Defect Termination in the UiO-66 Family of Metal–Organic Frameworks: The Role of Water and Modulator Tan, Kui; Pandey, Haardik; Wang, Hao Journal of the American Chemical Society, Vol. 143, Issue 17 https://doi.org/10.1021/jacs.1c01408	journal	April 2021
Beyond Radical Rebound: Methane Oxidation to Methanol Catalyzed by Iron Species in Metal–Organic Framework Nodes Simons, Matthew C.; Prinslow, Steven D.; Babucci, Melike Journal of the American Chemical Society, Vol. 143, Issue 31 https://doi.org/10.1021/jacs.1c04766	journal	July 2021
Structure–Activity Relationship Insights for Organophosphonate Hydrolysis at Ti(IV) Active Sites in Metal–Organic Frameworks Mian, Mohammad Rasel; Wang, Xijun; Wang, Xingjie Journal of the American Chemical Society, Vol. 145, Issue 13 https://doi.org/10.1021/jacs.2c13887	journal	March 2023
Unveiling Unexpected Modulator-CO₂ Dynamics within a Zirconium Metal–Organic Framework Rayder, Thomas M.; Formalik, Filip; Vornholt, Simon M. Journal of the American Chemical Society, Vol. 145, Issue 20 https://doi.org/10.1021/jacs.3c01146	journal	May 2023
Water-Accelerated Transport: Vapor-Phase Nerve Agent Simulant Delivery within a Catalytic Zirconium Metal–Organic Framework as a Function of Relative Humidity Wang, Rui; Shi, Kaihang; Liu, Jian Journal of the American Chemical Society https://doi.org/10.1021/jacs.3c03708	journal	June 2023
Temperature and Loading-Dependent Diffusion of Light Hydrocarbons in ZIF-8 as Predicted Through Fully Flexible Molecular Simulations Verploegh, Ross J.; Nair, Sankar; Sholl, David S. Journal of the American Chemical Society, Vol. 137, Issue 50 https://doi.org/10.1021/jacs.5b08746	journal	December 2015
Methane Oxidation to Methanol Catalyzed by Cu-Oxo Clusters Stabilized in NU-1000 Metal–Organic Framework Ikuno, Takaaki; Zheng, Jian; Vjunov, Aleksei Journal of the American Chemical Society, Vol. 139, Issue 30 https://doi.org/10.1021/jacs.7b02936	journal	July 2017
New Strategies for Direct Methane-to-Methanol Conversion from Active Learning Exploration of 16 Million Catalysts Nandy, Aditya; Duan, Chenru; Goffinet, Conrad JACS Au, Vol. 2, Issue 5 https://doi.org/10.1021/jacsau.2c00176	journal	April 2022
Estimating the Entropic Cost of Self-Assembly of Multiparticle Hydrogen-Bonded Aggregates Based on the Cyanuric Acid·Melamine Lattice Mammen, Mathai; Shakhnovich, Eugene I.; Deutch, John M. The Journal of Organic Chemistry, Vol. 63, Issue 12 https://doi.org/10.1021/jo970944f	journal	June 1998
United Atom Force Field for Alkanes in Nanoporous Materials Dubbeldam, D.; Calero, S.; Vlugt, T. J. H. The Journal of Physical Chemistry B, Vol. 108, Issue 33 https://doi.org/10.1021/jp0376727	journal	August 2004
Self-Diffusion and Transport Diffusion of Light Gases in Metal-Organic Framework Materials Assessed Using Molecular Dynamics Simulations Skoulidas, Anastasios I.; Sholl, David S. The Journal of Physical Chemistry B, Vol. 109, Issue 33 https://doi.org/10.1021/jp051771y	journal	August 2005
Force Field Validation for Molecular Dynamics Simulations of IRMOF-1 and Other Isoreticular Zinc Carboxylate Coordination Polymers Greathouse, Jeffery A.; Allendorf, Mark D. The Journal of Physical Chemistry C, Vol. 112, Issue 15 https://doi.org/10.1021/jp076853w	journal	April 2008
Understanding the Thermodynamic and Kinetic Behavior of the CO ₂ /CH ₄ Gas Mixture within the Porous Zirconium Terephthalate UiO-66(Zr): A Joint Experimental and Modeling Approach Yang, Qingyuan; Wiersum, Andrew D.; Jobic, Hervé The Journal of Physical Chemistry C, Vol. 115, Issue 28 https://doi.org/10.1021/jp202633t	journal	June 2011
On the Impact of Sorbent Mobility on the Sorbed Phase Equilibria and Dynamics: A Study of Methane and Carbon Dioxide within the Zeolite Imidazolate Framework-8 Pantatosaki, Evangelia; Megariotis, Grigorios; Pusch, Anne-Kristin The Journal of Physical Chemistry C, Vol. 116, Issue 1 https://doi.org/10.1021/jp207771s	journal	December 2011
Robust, Transferable, and Physically Motivated Force Fields for Gas Adsorption in Functionalized Zeolitic Imidazolate Frameworks McDaniel, Jesse G.; Schmidt, J. R. The Journal of Physical Chemistry C, Vol. 116, Issue 26 https://doi.org/10.1021/jp303790r	journal	June 2012
Physically-Motivated Force Fields from Symmetry-Adapted Perturbation Theory McDaniel, Jesse G.; Schmidt, J. R. The Journal of Physical Chemistry A, Vol. 117, Issue 10 https://doi.org/10.1021/jp3108182	journal	February 2013
Adsorption and Diffusion of CO ₂ and CH ₄ in Zeolitic Imidazolate Framework-8: Effect of Structural Flexibility Zhang, Liling; Wu, Gang; Jiang, Jianwen The Journal of Physical Chemistry C, Vol. 118, Issue 17 https://doi.org/10.1021/jp500796e	journal	April 2014
AuToGraFS: Automatic Topological Generator for Framework Structures Addicoat, Matthew A.; Coupry, Damien E.; Heine, Thomas The Journal of Physical Chemistry A, Vol. 118, Issue 40 https://doi.org/10.1021/jp507643v	journal	September 2014
Improved Force-Field Parameters for QM/MM Simulations of the Energies of Adsorption for Molecules in Zeolites and a Free Rotor Correction to the Rigid Rotor Harmonic Oscillator Model for Adsorption Enthalpies Li, Yi-Pei; Gomes, Joseph; Mallikarjun Sharada, Shaama The Journal of Physical Chemistry C, Vol. 119, Issue 4 https://doi.org/10.1021/jp509921r	journal	January 2015
A General Approach for Estimating Framework Charges in Metal−Organic Frameworks Xu, Qing; Zhong, Chongli The Journal of Physical Chemistry C, Vol. 114, Issue 11 https://doi.org/10.1021/jp910522h	journal	March 2010
An Extended Charge Equilibration Method Wilmer, Christopher E.; Kim, Ki Chul; Snurr, Randall Q. The Journal of Physical Chemistry Letters, Vol. 3, Issue 17 https://doi.org/10.1021/jz3008485	journal	August 2012
Fast and Accurate Electrostatics in Metal Organic Frameworks with a Robust Charge Equilibration Parameterization for High-Throughput Virtual Screening of Gas Adsorption Kadantsev, Eugene S.; Boyd, Peter G.; Daff, Thomas D. The Journal of Physical Chemistry Letters, Vol. 4, Issue 18 https://doi.org/10.1021/jz401479k	journal	August 2013
Rapid and Accurate Machine Learning Recognition of High Performing Metal Organic Frameworks for CO ₂ Capture Fernandez, Michael; Boyd, Peter G.; Daff, Thomas D. The Journal of Physical Chemistry Letters, Vol. 5, Issue 17 https://doi.org/10.1021/jz501331m	journal	August 2014
Defining the Proton Topology of the Zr₆-Based Metal–Organic Framework NU-1000 Planas, Nora; Mondloch, Joseph E.; Tussupbayev, Samat The Journal of Physical Chemistry Letters, Vol. 5, Issue 21, p. 3716-3723 https://doi.org/10.1021/jz501899j	journal	October 2014
Design of New Materials for Methane Storage Düren, Tina; Sarkisov, Lev; Yaghi, Omar M. Langmuir, Vol. 20, Issue 7, p. 2683-2689 https://doi.org/10.1021/la0355500	journal	March 2004
Molecular Dynamics Simulations on Gate Opening in ZIF-8: Identification of Factors for Ethane and Propane Separation Zheng, Bin; Pan, Yichang; Lai, Zhiping Langmuir, Vol. 29, Issue 28 https://doi.org/10.1021/la401015m	journal	June 2013
Efficient Methods for Screening of Metal Organic Framework Membranes for Gas Separations Using Atomically Detailed Models Keskin, Seda; Sholl, David S. Langmuir, Vol. 25, Issue 19 https://doi.org/10.1021/la901438x	journal	October 2009
Nanopore Structure and Sorption Properties of Cu−BTC Metal−Organic Framework Vishnyakov, Aleksey; Ravikovitch, Peter I.; Neimark, Alexander V. Nano Letters, Vol. 3, Issue 6 https://doi.org/10.1021/nl0341281	journal	June 2003
Structures and Formulæ of the Prussian Blues and Related Compounds Keggin, J. F.; Miles, F. D. Nature, Vol. 137, Issue 3466 https://doi.org/10.1038/137577a0	journal	April 1936
Design and synthesis of an exceptionally stable and highly porous metal-organic framework Li, Hailian; Eddaoudi, Mohamed; M., O'Keeffe Nature, Vol. 402, Issue 6759, p. 276-279 https://doi.org/10.1038/46248	journal	November 1999
A pressure-amplifying framework material with negative gas adsorption transitions Krause, Simon; Bon, Volodymyr; Senkovska, Irena Nature, Vol. 532, Issue 7599 https://doi.org/10.1038/nature17430	journal	April 2016
Large-scale screening of hypothetical metal–organic frameworks Wilmer, Christopher E.; Leaf, Michael; Lee, Chang Yeon Nature Chemistry, Vol. 4, Issue 2, p. 83-89 https://doi.org/10.1038/nchem.1192	journal	November 2011
Adsorbate-induced lattice deformation in IRMOF-74 series Jawahery, Sudi; Simon, Cory M.; Braun, Efrem Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/ncomms13945	journal	January 2017
Destruction of chemical warfare agents using metal–organic frameworks Mondloch, Joseph E.; Katz, Michael J.; Isley III, William C. Nature Materials, Vol. 14, Issue 5 https://doi.org/10.1038/nmat4238	journal	March 2015
High-throughput screening of hypothetical metal-organic frameworks for thermal conductivity Islamov, Meiirbek; Babaei, Hasan; Anderson, Ryther npj Computational Materials, Vol. 9, Issue 1 https://doi.org/10.1038/s41524-022-00961-x	journal	January 2023
Machine learning potentials for metal-organic frameworks using an incremental learning approach Vandenhaute, Sander; Cools-Ceuppens, Maarten; DeKeyser, Simon npj Computational Materials, Vol. 9, Issue 1 https://doi.org/10.1038/s41524-023-00969-x	journal	February 2023
Machine learned force-fields for an Ab-initio quality description of metal-organic frameworks Wieser, Sandro; Zojer, Egbert npj Computational Materials, Vol. 10, Issue 1 https://doi.org/10.1038/s41524-024-01205-w	journal	January 2024
Using collective knowledge to assign oxidation states of metal cations in metal–organic frameworks Jablonka, Kevin Maik; Ongari, Daniele; Moosavi, Seyed Mohamad Nature Chemistry, Vol. 13, Issue 8 https://doi.org/10.1038/s41557-021-00717-y	journal	July 2021
A data-science approach to predict the heat capacity of nanoporous materials Moosavi, Seyed Mohamad; Novotny, Balázs Álmos; Ongari, Daniele Nature Materials, Vol. 21, Issue 12 https://doi.org/10.1038/s41563-022-01374-3	journal	October 2022
Data-driven design of metal–organic frameworks for wet flue gas CO2 capture Boyd, Peter G.; Chidambaram, Arunraj; García-Díez, Enrique Nature, Vol. 576, Issue 7786 https://doi.org/10.1038/s41586-019-1798-7	journal	December 2019
CRAFTED: An exploratory database of simulated adsorption isotherms of metal-organic frameworks Oliveira, Felipe Lopes; Cleeton, Conor; Neumann Barros Ferreira, Rodrigo Scientific Data, Vol. 10, Issue 1 https://doi.org/10.1038/s41597-023-02116-z	journal	April 2023
Exploring the phase stability in interpenetrated diamondoid covalent organic frameworks Borgmans, Sander; Rogge, Sven M. J.; De Vos, Juul S. Communications Chemistry, Vol. 6, Issue 1 https://doi.org/10.1038/s42004-022-00808-y	journal	January 2023
CHGNet as a pretrained universal neural network potential for charge-informed atomistic modelling Deng, Bowen; Zhong, Peichen; Jun, KyuJung Nature Machine Intelligence, Vol. 5, Issue 9 https://doi.org/10.1038/s42256-023-00716-3	journal	September 2023
A universal graph deep learning interatomic potential for the periodic table Chen, Chi; Ong, Shyue Ping Nature Computational Science, Vol. 2, Issue 11 https://doi.org/10.1038/s43588-022-00349-3	journal	November 2022
A transferable recommender approach for selecting the best density functional approximations in chemical discovery Duan, Chenru; Nandy, Aditya; Meyer, Ralf Nature Computational Science, Vol. 3, Issue 1 https://doi.org/10.1038/s43588-022-00384-0	journal	December 2022
Evaluating metal–organic frameworks for natural gas storage Mason, Jarad A.; Veenstra, Mike; Long, Jeffrey R. Chemical Science, Vol. 5, Issue 1, p. 32-51 https://doi.org/10.1039/C3SC52633J	journal	January 2014
Acoustic phonons and negative thermal expansion in MOF-5 Rimmer, Leila H. N.; Dove, Martin T.; Goodwin, Andrew L. Phys. Chem. Chem. Phys., Vol. 16, Issue 39 https://doi.org/10.1039/C4CP01701C	journal	January 2014
Investigation of the terahertz vibrational modes of ZIF-8 and ZIF-90 with terahertz time-domain spectroscopy Tan, Nicholas Y.; Ruggiero, Michael T.; Orellana-Tavra, Claudia Chemical Communications, Vol. 51, Issue 89 https://doi.org/10.1039/C5CC06455D	journal	January 2015
Discovering connections between terahertz vibrations and elasticity underpinning the collective dynamics of the HKUST-1 metal–organic framework Ryder, Matthew R.; Civalleri, Bartolomeo; Cinque, Gianfelice CrystEngComm, Vol. 18, Issue 23 https://doi.org/10.1039/C5CE02347E	journal	January 2016
Molecular simulation of low temperature argon adsorption in several models of IRMOF-1 with defects and structural disorder Sarkisov, L. Dalton Transactions, Vol. 45, Issue 10 https://doi.org/10.1039/C5DT03498A	journal	January 2016
Explaining the mechanical mechanisms of zeolitic metal–organic frameworks: revealing auxeticity and anomalous elasticity Ryder, Matthew. R.; Tan, Jin-Chong Dalton Trans., Vol. 45, Issue 10 https://doi.org/10.1039/C5DT03514G	journal	January 2016
Benchmarking density functional theory predictions of framework structures and properties in a chemically diverse test set of metal–organic frameworks Nazarian, Dalar; Ganesh, P.; Sholl, David S. Journal of Materials Chemistry A, Vol. 3, Issue 44 https://doi.org/10.1039/C5TA03864B	journal	January 2015
A generalized method for constructing hypothetical nanoporous materials of any net topology from graph theory Boyd, Peter G.; Woo, Tom K. CrystEngComm, Vol. 18, Issue 21 https://doi.org/10.1039/C6CE00407E	journal	January 2016
A general forcefield for accurate phonon properties of metal–organic frameworks Bristow, Jessica K.; Skelton, Jonathan M.; Svane, Katrine L. Physical Chemistry Chemical Physics, Vol. 18, Issue 42 https://doi.org/10.1039/C6CP05106E	journal	January 2016
Introducing DDEC6 atomic population analysis: part 1. Charge partitioning theory and methodology Manz, Thomas A.; Limas, Nidia Gabaldon RSC Advances, Vol. 6, Issue 53 https://doi.org/10.1039/C6RA04656H	journal	January 2016
Introducing DDEC6 atomic population analysis: part 2. Computed results for a wide range of periodic and nonperiodic materials Limas, Nidia Gabaldon; Manz, Thomas A. RSC Advances, Vol. 6, Issue 51 https://doi.org/10.1039/C6RA05507A	journal	January 2016
Effect of pore size and shape on the thermal conductivity of metal-organic frameworks Babaei, Hasan; McGaughey, Alan J. H.; Wilmer, Christopher E. Chemical Science, Vol. 8, Issue 1 https://doi.org/10.1039/C6SC03704F	journal	January 2017
ANI-1: an extensible neural network potential with DFT accuracy at force field computational cost Smith, J. S.; Isayev, O.; Roitberg, A. E. Chemical Science, Vol. 8, Issue 4 https://doi.org/10.1039/C6SC05720A	journal	January 2017
Magnetic functionalities in MOFs: from the framework to the pore Mínguez Espallargas, Guillermo; Coronado, Eugenio Chemical Society Reviews, Vol. 47, Issue 2 https://doi.org/10.1039/C7CS00653E	journal	January 2018
Theoretical prediction of the mechanical properties of zeolitic imidazolate frameworks (ZIFs) Zheng, Bin; Zhu, Yihan; Fu, Fang RSC Advances, Vol. 7, Issue 66 https://doi.org/10.1039/C7RA07242B	journal	January 2017
Introducing DDEC6 atomic population analysis: part 3. Comprehensive method to compute bond orders Manz, Thomas A. RSC Adv., Vol. 7, Issue 72 https://doi.org/10.1039/C7RA07400J	journal	January 2017
Introducing DDEC6 atomic population analysis: part 4. Efficient parallel computation of net atomic charges, atomic spin moments, bond orders, and more Limas, Nidia Gabaldon; Manz, Thomas A. RSC Advances, Vol. 8, Issue 5 https://doi.org/10.1039/C7RA11829E	journal	January 2018
Increasing topological diversity during computational “synthesis” of porous crystals: how and why Anderson, Ryther; Gómez-Gualdrón, Diego A. CrystEngComm, Vol. 21, Issue 10 https://doi.org/10.1039/C8CE01637B	journal	January 2019
Large-scale computational assembly of ionic liquid/MOF composites: synergistic effect in the wire-tube conformation for efficient CO ₂ /CH ₄ separation Lan, Youshi; Yan, Tongan; Tong, Minman Journal of Materials Chemistry A, Vol. 7, Issue 20 https://doi.org/10.1039/C9TA01752F	journal	January 2019
Identifying misbonded atoms in the 2019 CoRE metal–organic framework database Chen, Taoyi; Manz, Thomas A. RSC Advances, Vol. 10, Issue 45 https://doi.org/10.1039/D0RA02498H	journal	January 2020
Nanoconfinement and mass transport in metal–organic frameworks Sharp, Conor H.; Bukowski, Brandon C.; Li, Hongyu Chemical Society Reviews, Vol. 50, Issue 20 https://doi.org/10.1039/D1CS00558H	journal	January 2021
Crystals springing into action: metal–organic framework CUK-1 as a pressure-driven molecular spring Iacomi, Paul; Lee, Ji Sun; Vanduyfhuys, Louis Chemical Science, Vol. 12, Issue 15 https://doi.org/10.1039/D1SC00205H	journal	January 2021
A systematic examination of the impacts of MOF flexibility on intracrystalline molecular diffusivities Yang, Yuhan; Sholl, David S. Journal of Materials Chemistry A, Vol. 10, Issue 8 https://doi.org/10.1039/D1TA09267G	journal	January 2022
Exploring mechanistic routes for light alkane oxidation with an iron–triazolate metal–organic framework Rosen, Andrew S.; Notestein, Justin M.; Snurr, Randall Q. Physical Chemistry Chemical Physics, Vol. 24, Issue 14 https://doi.org/10.1039/D2CP00963C	journal	January 2022
Benchmarking various types of partial atomic charges for classical all-atom simulations of metal–organic frameworks Liu, Sizhe; Luan, Binquan Nanoscale, Vol. 14, Issue 26 https://doi.org/10.1039/D2NR00354F	journal	January 2022
Unfolding the terahertz spectrum of soft porous crystals: rigid unit modes and their impact on phase transitions Hoffman, Alexander E. J.; Senkovska, Irena; Wieme, Jelle Journal of Materials Chemistry A, Vol. 10, Issue 33 https://doi.org/10.1039/D2TA01678H	journal	January 2022
Data mining for predicting gas diffusivity in zeolitic-imidazolate frameworks (ZIFs) Krokidas, Panagiotis; Karozis, Stelios; Moncho, Salvador Journal of Materials Chemistry A, Vol. 10, Issue 26 https://doi.org/10.1039/D2TA02624D	journal	January 2022
Synthesis, structure determination and properties of MIL-53as and MIL-53ht: the first Criii hybrid inorganic–organic microporous solids: Criii(OH)·{O2C–C6H4–CO2}·{HO2C–C6H4–CO2H}xElectronic supplementary information (ESI) available: crystal data, atomic coordinates and metrical parameters for MIL-53as and MIL-53ht. See http://www.rsc.org/suppdata/cc/b2/b201381a/ Millange, Franck; Serre, Christian; Férey, Gérard Chemical Communications, Issue 8 https://doi.org/10.1039/b201381a	journal	March 2002
A highly porous metal–organic framework, constructed from a cuboctahedral super-molecular building block, with exceptionally high methane uptake Stoeck, Ulrich; Krause, Simon; Bon, Volodymyr Chemical Communications, Vol. 48, Issue 88 https://doi.org/10.1039/c2cc34840c	journal	January 2012
Large breathing of the MOF MIL-47(VIV) under mechanical pressure: a joint experimental–modelling exploration Yot, Pascal G.; Ma, Qintian; Haines, Julien Chemical Science, Vol. 3, Issue 4 https://doi.org/10.1039/c2sc00745b	journal	January 2012
Improved tangent estimate in the nudged elastic band method for finding minimum energy paths and saddle points Henkelman, Graeme; Jónsson, Hannes The Journal of Chemical Physics, Vol. 113, Issue 22 https://doi.org/10.1063/1.1323224	journal	December 2000
A climbing image nudged elastic band method for finding saddle points and minimum energy paths Henkelman, Graeme; Uberuaga, Blas P.; Jónsson, Hannes The Journal of Chemical Physics, Vol. 113, Issue 22, p. 9901-9904 https://doi.org/10.1063/1.1329672	journal	December 2000
Equation of State Calculations by Fast Computing Machines Metropolis, Nicholas; Rosenbluth, Arianna W.; Rosenbluth, Marshall N. The Journal of Chemical Physics, Vol. 21, Issue 6 https://doi.org/10.1063/1.1699114	journal	June 1953
Markoff Random Processes and the Statistical Mechanics of Time‐Dependent Phenomena. II. Irreversible Processes in Fluids Green, Melville S. The Journal of Chemical Physics, Vol. 22, Issue 3 https://doi.org/10.1063/1.1740082	journal	March 1954
Computational study of hydrogen binding by metal-organic framework-5 Sagara, Tatsuhiko; Klassen, James; Ganz, Eric The Journal of Chemical Physics, Vol. 121, Issue 24 https://doi.org/10.1063/1.1809608	journal	January 2004
Superlinearly converging dimer method for transition state search Kästner, Johannes; Sherwood, Paul The Journal of Chemical Physics, Vol. 128, Issue 1 https://doi.org/10.1063/1.2815812	journal	January 2008
A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu Grimme, Stefan; Antony, Jens; Ehrlich, Stephan The Journal of Chemical Physics, Vol. 132, Issue 15 https://doi.org/10.1063/1.3382344	journal	April 2010
A generalized solid-state nudged elastic band method Sheppard, Daniel; Xiao, Penghao; Chemelewski, William The Journal of Chemical Physics, Vol. 136, Issue 7 https://doi.org/10.1063/1.3684549	journal	February 2012
Development of a force field for zeolitic imidazolate framework-8 with structural flexibility Hu, Zhongqiao; Zhang, Liling; Jiang, Jianwen The Journal of Chemical Physics, Vol. 136, Issue 24 https://doi.org/10.1063/1.4729314	journal	June 2012
Equilibrium molecular dynamics determination of thermal conductivity for multi-component systems Babaei, Hasan; Keblinski, Pawel; Khodadadi, Jay M. Journal of Applied Physics, Vol. 112, Issue 5 https://doi.org/10.1063/1.4749265	journal	September 2012
An efficient and near linear scaling pair natural orbital based local coupled cluster method Riplinger, Christoph; Neese, Frank The Journal of Chemical Physics, Vol. 138, Issue 3 https://doi.org/10.1063/1.4773581	journal	January 2013
A dimer method for finding saddle points on high dimensional potential surfaces using only first derivatives Henkelman, Graeme; Jónsson, Hannes The Journal of Chemical Physics, Vol. 111, Issue 15 https://doi.org/10.1063/1.480097	journal	October 1999
Benchmarking of GGA density functionals for modeling structures of nanoporous, rigid and flexible MOFs Formalik, Filip; Fischer, Michael; Rogacka, Justyna The Journal of Chemical Physics, Vol. 149, Issue 6 https://doi.org/10.1063/1.5030493	journal	August 2018
A generally applicable atomic-charge dependent London dispersion correction Caldeweyher, Eike; Ehlert, Sebastian; Hansen, Andreas The Journal of Chemical Physics, Vol. 150, Issue 15 https://doi.org/10.1063/1.5090222	journal	April 2019
Comparing GGA, GGA+ U , and meta-GGA functionals for redox-dependent binding at open metal sites in metal–organic frameworks Rosen, Andrew S.; Notestein, Justin M.; Snurr, Randall Q. The Journal of Chemical Physics, Vol. 152, Issue 22 https://doi.org/10.1063/5.0010166	journal	June 2020
Scalable molecular dynamics on CPU and GPU architectures with NAMD Phillips, James C.; Hardy, David J.; Maia, Julio D. C. The Journal of Chemical Physics, Vol. 153, Issue 4 https://doi.org/10.1063/5.0014475	journal	July 2020
When do short-range atomistic machine-learning models fall short? Yue, Shuwen; Muniz, Maria Carolina; Calegari Andrade, Marcos F. The Journal of Chemical Physics, Vol. 154, Issue 3 https://doi.org/10.1063/5.0031215	journal	January 2021
Exceptional chemical and thermal stability of zeolitic imidazolate frameworks Park, K. S.; Ni, Z.; Cote, A. P. Proceedings of the National Academy of Sciences, Vol. 103, Issue 27, p. 10186-10191 https://doi.org/10.1073/pnas.0602439103	journal	June 2006
Molecular modelling of adsorption in novel nanoporous metal–organic materials Sarkisov, Lev; Düren, Tina; Snurr, Randall Q. Molecular Physics, Vol. 102, Issue 2 https://doi.org/10.1080/00268970310001654854	journal	January 2004
Grand canonical ensemble Monte Carlo for a Lennard-Jones fluid Adams, D. J. Molecular Physics, Vol. 29, Issue 1 https://doi.org/10.1080/00268977500100221	journal	January 1975
Phase equilibria by simulation in the Gibbs ensemble: Alternative derivation, generalization and application to mixture and membrane equilibria Panagiotopoulos, A. Z.; Quirke, N.; Stapleton, M. Molecular Physics, Vol. 63, Issue 4 https://doi.org/10.1080/00268978800100361	journal	March 1988
On the inner workings of Monte Carlo codes Dubbeldam, David; Torres-Knoop, Ariana; Walton, Krista S. Molecular Simulation, Vol. 39, Issue 14-15 https://doi.org/10.1080/08927022.2013.819102	journal	December 2013
MCCCS Towhee: a tool for Monte Carlo molecular simulation Martin, Marcus G. Molecular Simulation, Vol. 39, Issue 14-15 https://doi.org/10.1080/08927022.2013.828208	journal	December 2013
DL_MONTE: a general purpose program for parallel Monte Carlo simulation Purton, J. A.; Crabtree, J. C.; Parker, S. C. Molecular Simulation, Vol. 39, Issue 14-15 https://doi.org/10.1080/08927022.2013.839871	journal	December 2013
An online parameter and property database for the TraPPE force field Eggimann, Becky L.; Sunnarborg, Amara J.; Stern, Hudson D. Molecular Simulation, Vol. 40, Issue 1-3 https://doi.org/10.1080/08927022.2013.842994	journal	December 2013
RASPA: molecular simulation software for adsorption and diffusion in flexible nanoporous materials Dubbeldam, David; Calero, Sofía; Ellis, Donald E. Molecular Simulation, Vol. 42, Issue 2 https://doi.org/10.1080/08927022.2015.1010082	journal	February 2015
Computer Simulation of Liquids Allen, Michael P.; Tildesley, Dominic J. https://doi.org/10.1093/oso/9780198803195.001.0001	book	June 2017
Electron correlations in narrow energy bands Hubbard, J. Proceedings of the Royal Society of London. Series A. Mathematical and Physical Sciences, Vol. 276, Issue 1365, p. 238-257 https://doi.org/10.1098/rspa.1963.0204	journal	November 1963
Inhomogeneous Electron Gas Hohenberg, P.; Kohn, W. Physical Review, Vol. 136, Issue 3B, p. B864-B871 https://doi.org/10.1103/PhysRev.136.B864	journal	November 1964
Self-Consistent Equations Including Exchange and Correlation Effects Kohn, W.; Sham, L. J. Physical Review, Vol. 140, Issue 4A, p. A1133-A1138 https://doi.org/10.1103/PhysRev.140.A1133	journal	November 1965
Workhorse minimally empirical dispersion-corrected density functional with tests for weakly bound systems: r2SCAN+rVV10 Ning, Jinliang; Kothakonda, Manish; Furness, James W. Physical Review B, Vol. 106, Issue 7 https://doi.org/10.1103/PhysRevB.106.075422	journal	August 2022
Comparison of atomic-level simulation methods for computing thermal conductivity Schelling, Patrick K.; Phillpot, Simon R.; Keblinski, Pawel Physical Review B, Vol. 65, Issue 14 https://doi.org/10.1103/PhysRevB.65.144306	journal	April 2002
First-principles phonon calculations of thermal expansion in Ti 3 SiC 2 , Ti 3 AlC 2 , and Ti 3 GeC 2 Togo, Atsushi; Chaput, Laurent; Tanaka, Isao Physical Review B, Vol. 81, Issue 17 https://doi.org/10.1103/PhysRevB.81.174301	journal	May 2010
Higher-accuracy van der Waals density functional Lee, Kyuho; Murray, Éamonn D.; Kong, Lingzhu Physical Review B, Vol. 82, Issue 8 https://doi.org/10.1103/PhysRevB.82.081101	journal	August 2010
Phonon-phonon interactions in transition metals Chaput, Laurent; Togo, Atsushi; Tanaka, Isao Physical Review B, Vol. 84, Issue 9 https://doi.org/10.1103/PhysRevB.84.094302	journal	September 2011
van der Waals density functional made accurate Hamada, Ikutaro Physical Review B, Vol. 89, Issue 12 https://doi.org/10.1103/PhysRevB.89.121103	journal	March 2014
Accurate Molecular Van Der Waals Interactions from Ground-State Electron Density and Free-Atom Reference Data Tkatchenko, Alexandre; Scheffler, Matthias Physical Review Letters, Vol. 102, Issue 7 https://doi.org/10.1103/PhysRevLett.102.073005	journal	February 2009
Gaussian Approximation Potentials: The Accuracy of Quantum Mechanics, without the Electrons Bartók, Albert P.; Payne, Mike C.; Kondor, Risi Physical Review Letters, Vol. 104, Issue 13 https://doi.org/10.1103/PhysRevLett.104.136403	journal	April 2010
Identifying the Role of Terahertz Vibrations in Metal-Organic Frameworks: From Gate-Opening Phenomenon to Shear-Driven Structural Destabilization Ryder, Matthew R.; Civalleri, Bartolomeo; Bennett, Thomas D. Physical Review Letters, Vol. 113, Issue 21 https://doi.org/10.1103/PhysRevLett.113.215502	journal	November 2014
Van der Waals Density Functional for General Geometries Dion, M.; Rydberg, H.; Schröder, E. Physical Review Letters, Vol. 92, Issue 24 https://doi.org/10.1103/PhysRevLett.92.246401	journal	June 2004
Generalized Neural-Network Representation of High-Dimensional Potential-Energy Surfaces Behler, Jörg; Parrinello, Michele Physical Review Letters, Vol. 98, Issue 14 https://doi.org/10.1103/PhysRevLett.98.146401	journal	April 2007
Hydrogen Storage in Microporous Metal-Organic Frameworks Rosi, Nathaniel L.; Eckert, Juergen; Eddaoudi, Mohamed Science, Vol. 300, Issue 5622, p. 1127-1129 https://doi.org/10.1126/science.1083440	journal	May 2003
Ultrahigh Porosity in Metal-Organic Frameworks Furukawa, H.; Ko, N.; Go, Y. B. Science, Vol. 329, Issue 5990, p. 424-428 https://doi.org/10.1126/science.1192160	journal	July 2010
Large-Pore Apertures in a Series of Metal-Organic Frameworks Deng, H.; Grunder, S.; Cordova, K. E. Science, Vol. 336, Issue 6084, p. 1018-1023 https://doi.org/10.1126/science.1220131	journal	May 2012
A Chemically Functionalizable Nanoporous Material [Cu₃(TMA)₂(H₂O)₃]_n Chui, Stephen S.-Y.; Lo, Samuel M.-F.; Charmant, Jonathan P. H. Science, Vol. 283, Issue 5405, p. 1148-1150 https://doi.org/10.1126/science.283.5405.1148	journal	February 1999
A scalable metal-organic framework as a durable physisorbent for carbon dioxide capture Lin, Jian-Bin; Nguyen, Tai T. T.; Vaidhyanathan, Ramanathan Science, Vol. 374, Issue 6574 https://doi.org/10.1126/science.abi7281	journal	December 2021
GoodVibes: automated thermochemistry for heterogeneous computational chemistry data Luchini, Guilian; Alegre-Requena, Juan V.; Funes-Ardoiz, Ignacio F1000Research, Vol. 9 https://doi.org/10.12688/f1000research.22758.1	journal	January 2020
Terminology of metal–organic frameworks and coordination polymers (IUPAC Recommendations 2013) Batten, Stuart R.; Champness, Neil R.; Chen, Xiao-Ming Pure and Applied Chemistry, Vol. 85, Issue 8 https://doi.org/10.1351/PAC-REC-12-11-20	journal	July 2013
The impact of lattice vibrations on the macroscopic breathing behavior of MIL-53(Al) Hoffman, Alexander E. J.; Wieme, Jelle; Rogge, Sven M. J. Zeitschrift für Kristallographie - Crystalline Materials, Vol. 234, Issue 7-8 https://doi.org/10.1515/zkri-2018-2154	journal	February 2019
Best Practices for Foundations in Molecular Simulations [Article v1.0] Braun, Efrem; Gilmer, Justin; Mayes, Heather B. Living Journal of Computational Molecular Science, Vol. 1, Issue 1 https://doi.org/10.33011/livecoms.1.1.5957	journal	January 2019

Similar Records

Machine Learned Force Field Modeling of Metal Organic Frameworks for CO2 Direct Air Capture

Conference · Tue Aug 06 00:00:00 EDT 2024 · OSTI ID:2426624

Reproducing Quantum Probability Distributions at the Speed of Classical Dynamics: A New Approach for Developing Force-Field Functors

Journal Article · Mon Mar 12 00:00:00 EDT 2018 · Journal of Physical Chemistry Letters · OSTI ID:1470507

Machine-Learned Force Field Modeling of Metal Organic Frameworks for CO2 Direct Air Capture

Conference · Wed Jun 19 00:00:00 EDT 2024 · OSTI ID:2375046

Related Subjects

36 MATERIALS SCIENCE
Monte Carlo simulation
density functional theory
machine learning
metal-organic frameworks
molecular dynamics simulation

Exploring the Structural, Dynamic, and Functional Properties of Metal–Organic Frameworks through Molecular Modeling

Citation Formats

References (238)

Similar Records

Related Subjects