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Kao YC, Wang YM, Yeh JY, Li SC, Wu KCW, Lin LC, Li YP. Tailoring parameters for QM/MM simulations: accurate modeling of adsorption and catalysis in zirconium-based metal-organic frameworks. Phys Chem Chem Phys 2024. [PMID: 39015995 DOI: 10.1039/d4cp00681j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
Quantum mechanics/molecular mechanics (QM/MM) simulations offer an efficient way to model reactions occurring in complex environments. This study introduces a specialized set of charge and Lennard-Jones parameters tailored for electrostatically embedded QM/MM calculations, aiming to accurately model both adsorption processes and catalytic reactions in zirconium-based metal-organic frameworks (Zr-MOFs). To validate our approach, we compare adsorption energies derived from QM/MM simulations against experimental results and Monte Carlo simulation outcomes. The developed parameters showcase the ability of QM/MM simulations to represent long-range electrostatic and van der Waals interactions faithfully. This capability is evidenced by the prediction of adsorption energies with a low root mean square error of 1.1 kcal mol-1 across a wide range of adsorbates. The practical applicability of our QM/MM model is further illustrated through the study of glucose isomerization and epimerization reactions catalyzed by two structurally distinct Zr-MOF catalysts, UiO-66 and MOF-808. Our QM/MM calculations closely align with experimental activation energies. Importantly, the parameter set introduced here is compatible with the widely used universal force field (UFF). Moreover, we thoroughly explore how the size of the cluster model and the choice of density functional theory (DFT) methodologies influence the simulation outcomes. This work provides an accurate and computationally efficient framework for modeling complex catalytic reactions within Zr-MOFs, contributing valuable insights into their mechanistic behaviors and facilitating further advancements in this dynamic area of research.
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Affiliation(s)
- Yu-Chi Kao
- Department of Chemical Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan.
| | - Yi-Ming Wang
- Department of Chemical Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan.
| | - Jyun-Yi Yeh
- Department of Chemical Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan.
- International Graduate Program of Molecular Science and Technology (NTU-MST), National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan
| | - Shih-Cheng Li
- Department of Chemical Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan.
| | - Kevin C-W Wu
- Department of Chemical Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan.
- International Graduate Program of Molecular Science and Technology (NTU-MST), National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan
- Department of Chemical Engineering and Materials Science, Yuan Ze University, Chung-Li, Taoyuan, Taiwan
| | - Li-Chiang Lin
- Department of Chemical Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan.
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, 151 West Woodruff Avenue, Columbus, OH, 43210-1350, USA
| | - Yi-Pei Li
- Department of Chemical Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan.
- Taiwan International Graduate Program on Sustainable Chemical Science and Technology (TIGP-SCST), No. 128, Sec. 2, Academia Road, Taipei, 11529, Taiwan
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Aljama HA, Head-Gordon M, Bell AT. Assessing the stability of Pd-exchanged sites in zeolites with the aid of a high throughput quantum chemistry workflow. Nat Commun 2022; 13:2910. [PMID: 35614062 PMCID: PMC9133006 DOI: 10.1038/s41467-022-29505-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 02/22/2022] [Indexed: 01/03/2023] Open
Abstract
Cation exchanged-zeolites are functional materials with a wide range of applications from catalysis to sorbents. They present a challenge for computational studies using density functional theory due to the numerous possible active sites. From Al configuration, to placement of extra framework cation(s), to potentially different oxidation states of the cation, accounting for all these possibilities is not trivial. To make the number of calculations more tractable, most studies focus on a few active sites. We attempt to go beyond these limitations by implementing a workflow for a high throughput screening, designed to systematize the problem and exhaustively search for feasible active sites. We use Pd-exchanged CHA and BEA to illustrate the approach. After conducting thousands of explicit DFT calculations, we identify the sites most favorable for the Pd cation and discuss the results in detail. The high throughput screening identifies many energetically favorable sites that are non-trivial. Lastly, we employ these results to examine NO adsorption in Pd-exchanged CHA, which is a promising passive NOx adsorbent (PNA) during the cold start of automobiles. The results shed light on critical active sites for NOx capture that were not previously studied.
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Affiliation(s)
- Hassan A Aljama
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA
| | - Martin Head-Gordon
- Department of Chemistry, University of California, Berkeley, CA, USA.
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Alexis T Bell
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA.
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Van der Mynsbrugge J, Head-Gordon M, Bell AT. Computational Modeling Predicts the Stability of Both Pd + and Pd 2+ Ion-Exchanged into H-CHA. JOURNAL OF MATERIALS CHEMISTRY. A 2021; 9:2161-2174. [PMID: 33686355 PMCID: PMC7936627 DOI: 10.1039/d0ta11254b] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Passive NOx adsorbers (PNA) using Pd/zeolites have emerged as a promising solution for the reduction of cold-start emissions from vehicle exhaust. However, the nature of the active sites and the mechanisms underlying NOx adsorption in Pd/zeolites remain a subject of ongoing investigation. In this study, we employ quantum chemical simulations to investigate the structure of Pd species in cation-exchange sites at isolated Al and Al pairs in the 6-ring and 8-ring of the CHA framework, before the introduction of NOx. Our calculations show that the speciation of Pd in these exchange sites strongly depends on the precise Al arrangement within the framework, as well as the operating conditions. Ionically dispersed Pd is found to be the most favorable species over a wide range of oxidizing and reducing conditions. Small oligomers of PdO and metallic Pd do not appear to be competitive at either isolated Al or Al pairs. Notably, our calculations show that ion exchange sites other than next-next-nearest neighbor Al pairs in the 6-ring will be preferentially occupied by Pd+ instead of Pd2+. The stability of Pd+ in the zeolite environment is an interesting contrast with its rareness in molecular Pd compounds. Nonetheless, a detailed analysis of the electronic structure shows that predicted Pd oxidation states are consistent with chemical intuition for all complexes investigated in this study. We also discuss the potential ambiguity in Pd characterization provided by typical experimental techniques such as XANES, EXAFS and UV-VIS, and highlight the need for additional EPR spectroscopy studies to further elucidate the initial Pd speciation in zeolites for PNA applications.
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Affiliation(s)
- Jeroen Van der Mynsbrugge
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA
| | - Martin Head-Gordon
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Alexis T. Bell
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA
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Nasluzov VA, Parker SM, Genest A, Shor AM, Ivanova-Shor EA, Rösch N. Trinuclear tantalum clusters grafted to hydroxylated silica surfaces: A density-functional embedded-cluster study. KINETICS AND CATALYSIS 2015. [DOI: 10.1134/s0023158415050134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Van Speybroeck V, Hemelsoet K, Joos L, Waroquier M, Bell RG, Catlow CRA. Advances in theory and their application within the field of zeolite chemistry. Chem Soc Rev 2015; 44:7044-111. [PMID: 25976164 DOI: 10.1039/c5cs00029g] [Citation(s) in RCA: 246] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Zeolites are versatile and fascinating materials which are vital for a wide range of industries, due to their unique structural and chemical properties, which are the basis of applications in gas separation, ion exchange and catalysis. Given their economic impact, there is a powerful incentive for smart design of new materials with enhanced functionalities to obtain the best material for a given application. Over the last decades, theoretical modeling has matured to a level that model guided design has become within reach. Major hurdles have been overcome to reach this point and almost all contemporary methods in computational materials chemistry are actively used in the field of modeling zeolite chemistry and applications. Integration of complementary modeling approaches is necessary to obtain reliable predictions and rationalizations from theory. A close synergy between experimentalists and theoreticians has led to a deep understanding of the complexity of the system at hand, but also allowed the identification of shortcomings in current theoretical approaches. Inspired by the importance of zeolite characterization which can now be performed at the single atom and single molecule level from experiment, computational spectroscopy has grown in importance in the last decade. In this review most of the currently available modeling tools are introduced and illustrated on the most challenging problems in zeolite science. Directions for future model developments will be given.
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Roscioni OM, Lee EPF, Dyke JM. Development and testing of a compact basis set for use in effective core potential calculations on rhodium complexes. J Comput Chem 2012; 33:2049-57. [DOI: 10.1002/jcc.23034] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Revised: 05/11/2012] [Accepted: 05/14/2012] [Indexed: 11/10/2022]
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Vayssilov GN, Petrova GP, Shor EAI, Nasluzov VA, Shor AM, Petkov PS, Rösch N. Reverse hydrogen spillover on and hydrogenation of supported metal clusters: insights from computational model studies. Phys Chem Chem Phys 2012; 14:5879-90. [DOI: 10.1039/c2cp23648f] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Zimmerman PM, Head-Gordon M, Bell AT. Selection and Validation of Charge and Lennard-Jones Parameters for QM/MM Simulations of Hydrocarbon Interactions with Zeolites. J Chem Theory Comput 2011; 7:1695-703. [DOI: 10.1021/ct2001655] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Paul M. Zimmerman
- Department of Chemistry, University of California, Berkeley, California 94720-1461, United States
| | - Martin Head-Gordon
- Department of Chemistry, University of California, Berkeley, California 94720-1461, United States
| | - Alexis T. Bell
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720-1462, United States
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Keal TW, Sherwood P, Dutta G, Sokol AA, Catlow CRA. Characterization of hydrogen dissociation over aluminium-doped zinc oxide using an efficient massively parallel framework for QM/MM calculations. Proc Math Phys Eng Sci 2011. [DOI: 10.1098/rspa.2010.0613] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A task-farm parallelization framework has been implemented in the ChemShell computational chemistry environment to provide a facility for parallelizing common chemical calculations, including finite-difference Hessian evaluation, the nudged elastic band method for reaction path optimization, and population-based methods for global optimization. The optimization methods are provided by a parallel interface to the DL-FIND optimization library. As ChemShell can already exploit parallel external programs for energy and gradient evaluations, the new methods result in a two-level approach to parallelization that gives significantly improved performance for massively parallel calculations. For typical systems, speed-up factors of five to eight times have been observed compared with non-task-farmed calculations. The task-farming version of ChemShell has been used to study the heterolytic dissociation of a hydrogen molecule over a polar oxygen-terminated surface of aluminium-doped zinc oxide using an embedded cluster hybrid QM/MM approach. We calculate a 42 kcal mol
−1
heat of reaction and a 30 kcal mol
−1
activation energy, which is equivalent to a high backward reaction barrier of 72 kcal mol
−1
per H
2
molecule, in close agreement with temperature programmed desorption experiments. The dissociation path includes a stable intermediate comprising a hydride ion in an oxygen vacancy and physisorbed atomic hydrogen.
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Affiliation(s)
- Thomas W. Keal
- Computational Science and Engineering Department, STFC Daresbury Laboratory, Daresbury, Warrington WA4 4AD, UK
| | - Paul Sherwood
- Computational Science and Engineering Department, STFC Daresbury Laboratory, Daresbury, Warrington WA4 4AD, UK
| | - Gargi Dutta
- Department of Chemistry, University College London, Kathleen Lonsdale Materials Chemistry, 20 Gordon Street, London WC1H 0AJ, UK
| | - Alexey A. Sokol
- Department of Chemistry, University College London, Kathleen Lonsdale Materials Chemistry, 20 Gordon Street, London WC1H 0AJ, UK
| | - C. Richard A. Catlow
- Department of Chemistry, University College London, Kathleen Lonsdale Materials Chemistry, 20 Gordon Street, London WC1H 0AJ, UK
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Sushko ML, Sushko PV, Abarenkov IV, Shluger AL. QM/MM method for metal-organic interfaces. J Comput Chem 2011; 31:2955-66. [PMID: 20645296 DOI: 10.1002/jcc.21591] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We present a QM/MM method for modeling metal/organic interfaces, which incorporates contributions from long-range electron correlation, characteristic to metals and non-bonded interactions in organic systems. This method can be used to study structurally irregular systems. We apply the method to model finite size domains of self-assembled monolayers on the gold (111) surface and discuss the influence of boundary effects on the electrostatic and electronic properties of these systems.
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Affiliation(s)
- Maria L Sushko
- London Centre for Nanotechnology and Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom.
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