1
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Zhao X, Xiao S, Yao B, Chen Y, Yu S. DFT-Based Mechanistic Exploration and Application in Photocatalytic Heterojunctions. J Chem Theory Comput 2024; 20:9770-9786. [PMID: 39509594 DOI: 10.1021/acs.jctc.4c01051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2024]
Abstract
Density functional theory (DFT) is one of the most widely used methods in the field of computational materials and has become an important research method for photocatalytic heterojunctions. Based on the research progress of DFT in the field of photocatalytic heterojunctions, this review introduces three kinds of heterojunction modeling in detail as well as the problems encountered in the construction process and the solutions. It provides a comprehensive review of the calculation methods of important parameters related to photocatalytic heterojunctions. Comparison, analysis, and discussion were conducted on some functional selections and calculation results based on experimental data. Finally, the limitations and shortcomings of DFT in the field of photocatalytic heterojunctions are pointed out. This review will provide valuable guidance for the calculation and analysis of the performance of photocatalytic heterojunctions and help promote the wider application of DFT in the field of photocatalysis.
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Affiliation(s)
- Xiang Zhao
- College of Material Science and Engineering, North China University of Science and Technology, Hebei, Tangshan 063210, China
| | - Shujuan Xiao
- College of Material Science and Engineering, North China University of Science and Technology, Hebei, Tangshan 063210, China
| | - Bingming Yao
- College of Material Science and Engineering, North China University of Science and Technology, Hebei, Tangshan 063210, China
| | - Yifu Chen
- College of Material Science and Engineering, North China University of Science and Technology, Hebei, Tangshan 063210, China
| | - Shouwu Yu
- College of Material Science and Engineering, North China University of Science and Technology, Hebei, Tangshan 063210, China
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2
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Al-Sakkari EG, Ragab A, Dagdougui H, Boffito DC, Amazouz M. Carbon capture, utilization and sequestration systems design and operation optimization: Assessment and perspectives of artificial intelligence opportunities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 917:170085. [PMID: 38224888 DOI: 10.1016/j.scitotenv.2024.170085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 12/10/2023] [Accepted: 01/09/2024] [Indexed: 01/17/2024]
Abstract
Carbon capture, utilization, and sequestration (CCUS) is a promising solution to decarbonize the energy and industrial sectors to mitigate climate change. An integrated assessment of technological options is required for the effective deployment of CCUS large-scale infrastructure between CO2 production and utilization/sequestration nodes. However, developing cost-effective strategies from engineering and operation perspectives to implement CCUS is challenging. This is due to the diversity of upstream emitting processes located in different geographical areas, available downstream utilization technologies, storage sites capacity/location, and current/future energy/emissions/economic conditions. This paper identifies the need to achieve a robust hybrid assessment tool for CCUS modeling, simulation, and optimization based mainly on artificial intelligence (AI) combined with mechanistic methods. Thus, a critical literature review is conducted to assess CCUS technologies and their related process modeling/simulation/optimization techniques, while evaluating the needs for improvements or new developments to reduce overall CCUS systems design and operation costs. These techniques include first principles- based and data-driven ones, i.e. AI and related machine learning (ML) methods. Besides, the paper gives an overview on the role of life cycle assessment (LCA) to evaluate CCUS systems where the combined LCA-AI approach is assessed. Other advanced methods based on the AI/ML capabilities/algorithms can be developed to optimize the whole CCUS value chain. Interpretable ML combined with explainable AI can accelerate optimum materials selection by giving strong rules which accelerates the design of capture/utilization plants afterwards. Besides, deep reinforcement learning (DRL) coupled with process simulations will accelerate process design/operation optimization through considering simultaneous optimization of equipment sizing and operating conditions. Moreover, generative deep learning (GDL) is a key solution to optimum capture/utilization materials design/discovery. The developed AI methods can be generalizable where the extracted knowledge can be transferred to future works to help cutting the costs of CCUS value chain.
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Affiliation(s)
- Eslam G Al-Sakkari
- Department of Mathematics and Industrial Engineering, Polytechnique Montréal, 2500 Chemin de Polytechnique, Montréal, Québec H3T 1J4, Canada; CanmetENERGY, 1615 Lionel-Boulet Blvd, P.O. Box 4800, Varennes, Québec J3X 1P7, Canada.
| | - Ahmed Ragab
- Department of Mathematics and Industrial Engineering, Polytechnique Montréal, 2500 Chemin de Polytechnique, Montréal, Québec H3T 1J4, Canada; CanmetENERGY, 1615 Lionel-Boulet Blvd, P.O. Box 4800, Varennes, Québec J3X 1P7, Canada
| | - Hanane Dagdougui
- Department of Mathematics and Industrial Engineering, Polytechnique Montréal, 2500 Chemin de Polytechnique, Montréal, Québec H3T 1J4, Canada
| | - Daria C Boffito
- Department of Chemical Engineering, Polytechnique Montréal, 2500 Chemin de Polytechnique, Montréal, Québec H3T 1J4, Canada; Canada Research Chair in Engineering Process Intensification and Catalysis (EPIC), Canada
| | - Mouloud Amazouz
- CanmetENERGY, 1615 Lionel-Boulet Blvd, P.O. Box 4800, Varennes, Québec J3X 1P7, Canada
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3
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Rey J, Chizallet C, Rocca D, Bučko T, Badawi M. Reference-Quality Free Energy Barriers in Catalysis from Machine Learning Thermodynamic Perturbation Theory. Angew Chem Int Ed Engl 2024; 63:e202312392. [PMID: 38055209 DOI: 10.1002/anie.202312392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 11/11/2023] [Accepted: 12/06/2023] [Indexed: 12/07/2023]
Abstract
For the first time, we report calculations of the free energies of activation of cracking and isomerization reactions of alkenes that combine several different electronic structure methods with molecular dynamics simulations. We demonstrate that the use of a high level of theory (here Random Phase Approximation-RPA) is necessary to bridge the gap between experimental and computed values. These transformations, catalyzed by zeolites and proceeding via cationic intermediates and transition states, are building blocks of many chemical transformations for valorization of long chain paraffins originating, e.g., from plastic waste, vegetable oils, Fischer-Tropsch waxes or crude oils. Compared with the free energy barriers computed at the PBE+D2 production level of theory via constrained ab initio molecular dynamics, the barriers computed at the RPA level by the application of Machine Learning thermodynamic Perturbation Theory (MLPT) show a significant decrease for isomerization reaction and an increase of a similar magnitude for cracking, yielding an unprecedented agreement with the results obtained by experiments and kinetic modeling.
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Affiliation(s)
- Jérôme Rey
- Laboratoire de Physique et Chimie Théoriques LPCT UMR 7019-CNRS, Université de Lorraine, Vandœuvre-lés-Nancy, France
| | - Céline Chizallet
- IFP Energies nouvelles, Rond-Point de l'Ēchangeur de Solaize, BP3, 69360, Solaize, France
| | - Dario Rocca
- Laboratoire de Physique et Chimie Théoriques LPCT UMR 7019-CNRS, Université de Lorraine, Vandœuvre-lés-Nancy, France
| | - Tomáš Bučko
- Department of Physical and Theoretical Chemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, SK-84215, Bratislava, Slovakia
- Institute of Inorganic Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, SK-84236, Bratislava, Slovakia
| | - Michael Badawi
- Laboratoire de Physique et Chimie Théoriques LPCT UMR 7019-CNRS, Université de Lorraine, Vandœuvre-lés-Nancy, France
- Laboratoire Lorrain de Chimie Moléculaire L2CM UMR 7053-CNRS, Université de Lorraine, Metz, France
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4
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Rizzi A, Carloni P, Parrinello M. Free energies at QM accuracy from force fields via multimap targeted estimation. Proc Natl Acad Sci U S A 2023; 120:e2304308120. [PMID: 37931103 PMCID: PMC10655219 DOI: 10.1073/pnas.2304308120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 09/25/2023] [Indexed: 11/08/2023] Open
Abstract
Accurate predictions of ligand binding affinities would greatly accelerate the first stages of drug discovery campaigns. However, using highly accurate interatomic potentials based on quantum mechanics (QM) in free energy methods has been so far largely unfeasible due to their prohibitive computational cost. Here, we present an efficient method to compute QM free energies from simulations using cheap reference potentials, such as force fields (FFs). This task has traditionally been out of reach due to the slow convergence of computing the correction from the FF to the QM potential. To overcome this bottleneck, we generalize targeted free energy methods to employ multiple maps-implemented with normalizing flow neural networks (NNs)-that maximize the overlap between the distributions. Critically, the method requires neither a separate expensive training phase for the NNs nor samples from the QM potential. We further propose a one-epoch learning policy to efficiently avoid overfitting, and we combine our approach with enhanced sampling strategies to overcome the pervasive problem of poor convergence due to slow degrees of freedom. On the drug-like molecules in the HiPen dataset, the method accelerates the calculation of the free energy difference of switching from an FF to a DFTB3 potential by three orders of magnitude compared to standard free energy perturbation and by a factor of eight compared to previously published nonequilibrium calculations. Our results suggest that our method, in combination with efficient QM/MM calculations, may be used in lead optimization campaigns in drug discovery and to study protein-ligand molecular recognition processes.
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Affiliation(s)
- Andrea Rizzi
- Computational Biomedicine, Institute of Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Jülich52428, Germany
- Atomistic Simulations, Italian Institute of Technology, Genova16163, Italy
| | - Paolo Carloni
- Computational Biomedicine, Institute of Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Jülich52428, Germany
- Department of Physics and Universitätsklinikum, RWTH Aachen University, Aachen52074, Germany
| | - Michele Parrinello
- Atomistic Simulations, Italian Institute of Technology, Genova16163, Italy
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Van Speybroeck V, Bocus M, Cnudde P, Vanduyfhuys L. Operando Modeling of Zeolite-Catalyzed Reactions Using First-Principles Molecular Dynamics Simulations. ACS Catal 2023; 13:11455-11493. [PMID: 37671178 PMCID: PMC10476167 DOI: 10.1021/acscatal.3c01945] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 07/27/2023] [Indexed: 09/07/2023]
Abstract
Within this Perspective, we critically reflect on the role of first-principles molecular dynamics (MD) simulations in unraveling the catalytic function within zeolites under operating conditions. First-principles MD simulations refer to methods where the dynamics of the nuclei is followed in time by integrating the Newtonian equations of motion on a potential energy surface that is determined by solving the quantum-mechanical many-body problem for the electrons. Catalytic solids used in industrial applications show an intriguing high degree of complexity, with phenomena taking place at a broad range of length and time scales. Additionally, the state and function of a catalyst critically depend on the operating conditions, such as temperature, moisture, presence of water, etc. Herein we show by means of a series of exemplary cases how first-principles MD simulations are instrumental to unravel the catalyst complexity at the molecular scale. Examples show how the nature of reactive species at higher catalytic temperatures may drastically change compared to species at lower temperatures and how the nature of active sites may dynamically change upon exposure to water. To simulate rare events, first-principles MD simulations need to be used in combination with enhanced sampling techniques to efficiently sample low-probability regions of phase space. Using these techniques, it is shown how competitive pathways at operating conditions can be discovered and how broad transition state regions can be explored. Interestingly, such simulations can also be used to study hindered diffusion under operating conditions. The cases shown clearly illustrate how first-principles MD simulations reveal insights into the catalytic function at operating conditions, which could not be discovered using static or local approaches where only a few points are considered on the potential energy surface (PES). Despite these advantages, some major hurdles still exist to fully integrate first-principles MD methods in a standard computational catalytic workflow or to use the output of MD simulations as input for multiple length/time scale methods that aim to bridge to the reactor scale. First of all, methods are needed that allow us to evaluate the interatomic forces with quantum-mechanical accuracy, albeit at a much lower computational cost compared to currently used density functional theory (DFT) methods. The use of DFT limits the currently attainable length/time scales to hundreds of picoseconds and a few nanometers, which are much smaller than realistic catalyst particle dimensions and time scales encountered in the catalysis process. One solution could be to construct machine learning potentials (MLPs), where a numerical potential is derived from underlying quantum-mechanical data, which could be used in subsequent MD simulations. As such, much longer length and time scales could be reached; however, quite some research is still necessary to construct MLPs for the complex systems encountered in industrially used catalysts. Second, most currently used enhanced sampling techniques in catalysis make use of collective variables (CVs), which are mostly determined based on chemical intuition. To explore complex reactive networks with MD simulations, methods are needed that allow the automatic discovery of CVs or methods that do not rely on a priori definition of CVs. Recently, various data-driven methods have been proposed, which could be explored for complex catalytic systems. Lastly, first-principles MD methods are currently mostly used to investigate local reactive events. We hope that with the rise of data-driven methods and more efficient methods to describe the PES, first-principles MD methods will in the future also be able to describe longer length/time scale processes in catalysis. This might lead to a consistent dynamic description of all steps-diffusion, adsorption, and reaction-as they take place at the catalyst particle level.
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Affiliation(s)
| | - Massimo Bocus
- Center for Molecular Modeling, Ghent University, Technologiepark 46, 9052 Zwijnaarde, Belgium
| | - Pieter Cnudde
- Center for Molecular Modeling, Ghent University, Technologiepark 46, 9052 Zwijnaarde, Belgium
| | - Louis Vanduyfhuys
- Center for Molecular Modeling, Ghent University, Technologiepark 46, 9052 Zwijnaarde, Belgium
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6
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Van Speybroeck V. Challenges in modelling dynamic processes in realistic nanostructured materials at operating conditions. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2023; 381:20220239. [PMID: 37211031 PMCID: PMC10200353 DOI: 10.1098/rsta.2022.0239] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 01/23/2023] [Indexed: 05/23/2023]
Abstract
The question is addressed in how far current modelling strategies are capable of modelling dynamic phenomena in realistic nanostructured materials at operating conditions. Nanostructured materials used in applications are far from perfect; they possess a broad range of heterogeneities in space and time extending over several orders of magnitude. Spatial heterogeneities from the subnanometre to the micrometre scale in crystal particles with a finite size and specific morphology, impact the material's dynamics. Furthermore, the material's functional behaviour is largely determined by the operating conditions. Currently, there exists a huge length-time scale gap between attainable theoretical length-time scales and experimentally relevant scales. Within this perspective, three key challenges are highlighted within the molecular modelling chain to bridge this length-time scale gap. Methods are needed that enable (i) building structural models for realistic crystal particles having mesoscale dimensions with isolated defects, correlated nanoregions, mesoporosity, internal and external surfaces; (ii) the evaluation of interatomic forces with quantum mechanical accuracy albeit at much lower computational cost than the currently used density functional theory methods and (iii) derivation of the kinetics of phenomena taking place in a multi-length-time scale window to obtain an overall view of the dynamics of the process. This article is part of a discussion meeting issue 'Supercomputing simulations of advanced materials'.
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7
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Chizallet C, Bouchy C, Larmier K, Pirngruber G. Molecular Views on Mechanisms of Brønsted Acid-Catalyzed Reactions in Zeolites. Chem Rev 2023; 123:6107-6196. [PMID: 36996355 DOI: 10.1021/acs.chemrev.2c00896] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/01/2023]
Abstract
The Brønsted acidity of proton-exchanged zeolites has historically led to the most impactful applications of these materials in heterogeneous catalysis, mainly in the fields of transformations of hydrocarbons and oxygenates. Unravelling the mechanisms at the atomic scale of these transformations has been the object of tremendous efforts in the last decades. Such investigations have extended our fundamental knowledge about the respective roles of acidity and confinement in the catalytic properties of proton exchanged zeolites. The emerging concepts are of general relevance at the crossroad of heterogeneous catalysis and molecular chemistry. In the present review, emphasis is given to molecular views on the mechanism of generic transformations catalyzed by Brønsted acid sites of zeolites, combining the information gained from advanced kinetic analysis, in situ, and operando spectroscopies, and quantum chemistry calculations. After reviewing the current knowledge on the nature of the Brønsted acid sites themselves, and the key parameters in catalysis by zeolites, a focus is made on reactions undergone by alkenes, alkanes, aromatic molecules, alcohols, and polyhydroxy molecules. Elementary events of C-C, C-H, and C-O bond breaking and formation are at the core of these reactions. Outlooks are given to take up the future challenges in the field, aiming at getting ever more accurate views on these mechanisms, and as the ultimate goal, to provide rational tools for the design of improved zeolite-based Brønsted acid catalysts.
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Affiliation(s)
- Céline Chizallet
- IFP Energies nouvelles, Rond-Point de l'Echangeur de Solaize, BP 3, Solaize 69360, France
| | - Christophe Bouchy
- IFP Energies nouvelles, Rond-Point de l'Echangeur de Solaize, BP 3, Solaize 69360, France
| | - Kim Larmier
- IFP Energies nouvelles, Rond-Point de l'Echangeur de Solaize, BP 3, Solaize 69360, France
| | - Gerhard Pirngruber
- IFP Energies nouvelles, Rond-Point de l'Echangeur de Solaize, BP 3, Solaize 69360, France
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8
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Berger F, Rybicki M, Sauer J. Molecular Dynamics with Chemical Accuracy─Alkane Adsorption in Acidic Zeolites. ACS Catal 2023. [DOI: 10.1021/acscatal.2c05493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Fabian Berger
- Institut für Chemie, Humboldt-Universität zu Berlin, D-10099Berlin, Germany
| | - Marcin Rybicki
- Institut für Chemie, Humboldt-Universität zu Berlin, D-10099Berlin, Germany
| | - Joachim Sauer
- Institut für Chemie, Humboldt-Universität zu Berlin, D-10099Berlin, Germany
- Department of Physical and Macromolecular Chemistry & Charles University Center of Advanced Materials, Charles University, Hlavova 8, 128 43Prague 2, Czech Republic
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9
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Giese TJ, Zeng J, York DM. Multireference Generalization of the Weighted Thermodynamic Perturbation Method. J Phys Chem A 2022; 126:8519-8533. [PMID: 36301936 PMCID: PMC9771595 DOI: 10.1021/acs.jpca.2c06201] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We describe the generalized weighted thermodynamic perturbation (gwTP) method for estimating the free energy surface of an expensive "high-level" potential energy function from the umbrella sampling performed with multiple inexpensive "low-level" reference potentials. The gwTP method is a generalization of the weighted thermodynamic perturbation (wTP) method developed by Li and co-workers [J. Chem. Theory Comput. 2018, 14, 5583-5596] that uses a single "low-level" reference potential. The gwTP method offers new possibilities in model design whereby the sampling generated from several low-level potentials may be combined (e.g., specific reaction parameter models that might have variable accuracy at different stages of a multistep reaction). The gwTP method is especially well suited for use with machine learning potentials (MLPs) that are trained against computationally expensive ab initio quantum mechanical/molecular mechanical (QM/MM) energies and forces using active learning procedures that naturally produce multiple distinct neural network potentials. Simulations can be performed with greater sampling using the fast MLPs and then corrected to the ab initio level using gwTP. The capabilities of the gwTP method are demonstrated by creating reference potentials based on the MNDO/d and DFTB2/MIO semiempirical models supplemented with the "range-corrected deep potential" (DPRc). The DPRc parameters are trained to ab initio QM/MM data, and the potentials are used to calculate the free energy surface of stepwise mechanisms for nonenzymatic RNA 2'-O-transesterification model reactions. The extended sampling made possible by the reference potentials allows one to identify unequilibrated portions of the simulations that are not always evident from the short time scale commonly used with ab initio QM/MM potentials. We show that the reference potential approach can yield more accurate ab initio free energy predictions than the wTP method or what can be reasonably afforded from explicit ab initio QM/MM sampling.
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Affiliation(s)
- Timothy J. Giese
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Jinzhe Zeng
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Darrin M. York
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
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10
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Gešvandtnerová M, Bučko T, Raybaud P, Chizallet C. Monomolecular mechanisms of isobutanol conversion to butenes catalyzed by acidic zeolites: alcohol isomerization as a key to the production of linear butenes. J Catal 2022. [DOI: 10.1016/j.jcat.2022.07.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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11
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Chen W, Yi X, Liu Z, Tang X, Zheng A. Carbocation chemistry confined in zeolites: spectroscopic and theoretical characterizations. Chem Soc Rev 2022; 51:4337-4385. [PMID: 35536126 DOI: 10.1039/d1cs00966d] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Acid-catalyzed reactions inside zeolites are one type of broadly applied industrial reactions, where carbocations are the most common intermediates of these reaction processes, including methanol to olefins, alkene/aromatic alkylation, and hydrocarbon cracking/isomerization. The fundamental research on these acid-catalyzed reactions is focused on the stability, evolution, and lifetime of carbocations under the zeolite confinement effect, which greatly affects the efficiency, selectivity and deactivation of zeolite catalysts. Therefore, a profound understanding of the carbocations confined in zeolites is not only beneficial to explain the reaction mechanism but also drive the design of new zeolite catalysts with ideal acidity and cages/channels. In this review, we provide both an in-depth understanding of the stabilization of carbocations by the pore confinement effect and summary of the advanced characterization methods to capture carbocations in zeolites, including UV-vis spectroscopy, solid-state NMR, fluorescence microscopy, IR spectroscopy and Raman spectroscopy. Also, we clarify the relationship between the activity and stability of carbocations in zeolite-catalyzed reactions, and further highlight the role of carbocations in various hydrocarbon conversion reactions inside zeolites with diverse frameworks and varying acidic properties.
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Affiliation(s)
- Wei Chen
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, P. R. China.
| | - Xianfeng Yi
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, P. R. China.
| | - Zhiqiang Liu
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, P. R. China.
| | - Xiaomin Tang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, P. R. China.
| | - Anmin Zheng
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, P. R. China. .,University of Chinese Academy of Sciences, Beijing 100049, P. R. China
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12
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Sundararaman R, Vigil-Fowler D, Schwarz K. Improving the Accuracy of Atomistic Simulations of the Electrochemical Interface. Chem Rev 2022; 122:10651-10674. [PMID: 35522135 PMCID: PMC10127457 DOI: 10.1021/acs.chemrev.1c00800] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Atomistic simulation of the electrochemical double layer is an ambitious undertaking, requiring quantum mechanical description of electrons, phase space sampling of liquid electrolytes, and equilibration of electrolytes over nanosecond time scales. All models of electrochemistry make different trade-offs in the approximation of electrons and atomic configurations, from the extremes of classical molecular dynamics of a complete interface with point-charge atoms to correlated electronic structure methods of a single electrode configuration with no dynamics or electrolyte. Here, we review the spectrum of simulation techniques suitable for electrochemistry, focusing on the key approximations and accuracy considerations for each technique. We discuss promising approaches, such as enhanced sampling techniques for atomic configurations and computationally efficient beyond density functional theory (DFT) electronic methods, that will push electrochemical simulations beyond the present frontier.
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Affiliation(s)
- Ravishankar Sundararaman
- Department of Materials Science and Engineering, Rensselaer Polytechnic Institute, 110 8th Street, Troy, New York 12180, United States
| | - Derek Vigil-Fowler
- Materials, Chemical, and Computational Science Directorate, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Kathleen Schwarz
- Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
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13
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Recent advances in the application of machine-learning algorithms to predict adsorption energies. TRENDS IN CHEMISTRY 2022. [DOI: 10.1016/j.trechm.2022.01.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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14
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Zech A, Bazhirov T. CateCom: A Practical Data-Centric Approach to Categorization of Computational Models. J Chem Inf Model 2022; 62:1268-1281. [PMID: 35230849 DOI: 10.1021/acs.jcim.2c00112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The advent of data-driven science in the 21st century brought about the need for well-organized structured data and associated infrastructure able to facilitate the applications of artificial intelligence and machine learning. We present an effort aimed at organizing the diverse landscape of physics-based and data-driven computational models in order to facilitate the storage of associated information as structured data. We apply object-oriented design concepts and outline the foundations of an open-source collaborative framework that is (1) capable of uniquely describing the approaches in structured data, (2) flexible enough to cover the majority of widely used models, and (3) utilizes collective intelligence through community contributions. We present example database schemas and corresponding data structures and explain how these are deployed in software at the time of this writing.
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Affiliation(s)
- Alexander Zech
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Timur Bazhirov
- Exabyte Inc., San Francisco, California 94105, United States
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15
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Herzog B, Chagas da Silva M, Casier B, Badawi M, Pascale F, Bučko T, Lebègue S, Rocca D. Assessing the Accuracy of Machine Learning Thermodynamic Perturbation Theory: Density Functional Theory and Beyond. J Chem Theory Comput 2022; 18:1382-1394. [PMID: 35191699 DOI: 10.1021/acs.jctc.1c01034] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Machine learning thermodynamic perturbation theory (MLPT) is a promising approach to compute finite temperature properties when the goal is to compare several different levels of ab initio theory and/or to apply highly expensive computational methods. Indeed, starting from a production molecular dynamics trajectory, this method can estimate properties at one or more target levels of theory from only a small number of additional fixed-geometry calculations, which are used to train a machine learning model. However, as MLPT is based on thermodynamic perturbation theory (TPT), inaccuracies might arise when the starting point trajectory samples a configurational space which has a small overlap with that of the target approximations of interest. By considering case studies of molecules adsorbed in zeolites and several different density functional theory approximations, in this work we assess the accuracy of MLPT for ensemble total energies and enthalpies of adsorption. It is shown that problematic cases can be detected even without knowing reference results and that even in these situations it is possible to recover target level results within chemical accuracy by applying a machine-learning-based Monte Carlo (MLMC) resampling. Finally, on the basis of the ideas developed in this work, we assess and confirm the accuracy of recently published MLPT-based enthalpies of adsorption at the random phase approximation level, whose high computational cost would completely hinder a direct molecular dynamics simulation.
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Affiliation(s)
- Basile Herzog
- Université de Lorraine and CNRS, Laboratoire de Physique et Chimie Théorique, UMR 7019, 54506 Vandœuvre-lés-Nancy, France
| | - Maurício Chagas da Silva
- Université de Lorraine and CNRS, Laboratoire de Physique et Chimie Théorique, UMR 7019, 54506 Vandœuvre-lés-Nancy, France
| | - Bastien Casier
- Université de Lorraine and CNRS, Laboratoire de Physique et Chimie Théorique, UMR 7019, 54506 Vandœuvre-lés-Nancy, France
| | - Michael Badawi
- Université de Lorraine and CNRS, Laboratoire de Physique et Chimie Théorique, UMR 7019, 54506 Vandœuvre-lés-Nancy, France
| | - Fabien Pascale
- Université de Lorraine and CNRS, Laboratoire de Physique et Chimie Théorique, UMR 7019, 54506 Vandœuvre-lés-Nancy, France
| | - Tomáš Bučko
- Department of Physical and Theoretical Chemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská Dolina, Ilkovičova 6, SK-84215 Bratislava, Slovakia.,Institute of Inorganic Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, SK-84236 Bratislava, Slovakia
| | - Sébastien Lebègue
- Université de Lorraine and CNRS, Laboratoire de Physique et Chimie Théorique, UMR 7019, 54506 Vandœuvre-lés-Nancy, France
| | - Dario Rocca
- Université de Lorraine and CNRS, Laboratoire de Physique et Chimie Théorique, UMR 7019, 54506 Vandœuvre-lés-Nancy, France
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16
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Saini V, Sharma A, Nivatia D. A machine learning approach for predicting the nucleophilicity of organic molecules. Phys Chem Chem Phys 2022; 24:1821-1829. [PMID: 34986215 DOI: 10.1039/d1cp05072a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Nucleophilicity provides important information about the chemical reactivity of organic molecules. Experimental determination of the nucleophilicity parameter is a tedious and resource-intensive approach. Herein, we present a novel machine learning protocol that uses key structural descriptors to predict the nucleophilicities of organic molecules, which agree well with the experimental values. A data driven approach was used where quantum mechanical molecular and thermodynamic descriptors from a wide range of structurally diverse nucleophiles and relevant solvents were extracted and modelled using advanced algorithms against the experimentally available nucleophilicity values. Despite the structural diversity of nucleophiles, we are able to achieve statistically robust models with a high predictive power using tree-based and neural network algorithms trained on an in-house developed unique dataset consisting of 752 nucleophilicity values and 27 molecular descriptors.
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Affiliation(s)
- Vaneet Saini
- Department of Chemistry & Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh 160014, India.
| | - Aditya Sharma
- Department of Chemistry & Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh 160014, India.
| | - Dhruv Nivatia
- IT Department, University Institute of Engineering & Technology, Panjab University, Chandigarh 160014, India
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17
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Rizzi A, Carloni P, Parrinello M. Targeted Free Energy Perturbation Revisited: Accurate Free Energies from Mapped Reference Potentials. J Phys Chem Lett 2021; 12:9449-9454. [PMID: 34555284 DOI: 10.1021/acs.jpclett.1c02135] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We present an approach that extends the theory of targeted free energy perturbation (TFEP) to calculate free energy differences and free energy surfaces at an accurate quantum mechanical level of theory from a cheaper reference potential. The convergence is accelerated by a mapping function that increases the overlap between the target and the reference distributions. Building on recent work, we show that this map can be learned with a normalizing flow neural network, without requiring simulations with the expensive target potential but only a small number of single-point calculations, and, crucially, avoiding the systematic error that was found previously. We validate the method by numerically evaluating the free energy difference in a system with a double-well potential and by describing the free energy landscape of a simple chemical reaction in the gas phase.
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Affiliation(s)
- Andrea Rizzi
- Computational Biomedicine, Institute of Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Jülich 52428, Germany
- Atomistic Simulations, Italian Institute of Technology, Via Morego 30, Genova 16163, Italy
| | - Paolo Carloni
- Computational Biomedicine, Institute of Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Jülich 52428, Germany
- Molecular Neuroscience and Neuroimaging (INM-11), Forschungszentrum Jülich GmbH, Jülich 52428, Germany
- Department of Physics and Universitätsklinikum, RWTH Aachen University, Aachen 52074, Germany
| | - Michele Parrinello
- Atomistic Simulations, Italian Institute of Technology, Via Morego 30, Genova 16163, Italy
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18
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Achievements and Expectations in the Field of Computational Heterogeneous Catalysis in an Innovation Context. Top Catal 2021. [DOI: 10.1007/s11244-021-01489-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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19
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Rybkin VV. Formulation and Implementation of Density Functional Embedding Theory Using Products of Basis Functions. J Chem Theory Comput 2021; 17:3995-4005. [PMID: 34048247 DOI: 10.1021/acs.jctc.1c00175] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The representation of embedding potential using products of atomic orbital basis functions has been developed in the context of density functional embedding theory. The formalism allows to treat pseudopotential and all-electron calculations on the same footing and enables simple transfer of the embedding potential in a compact matrix form. In addition, a cost-reduction procedure for the basis set and potential reduction based on population analysis has been proposed. Implemented for the condensed-phase and molecular systems within Gaussian and plane-waves and Gaussian and augmented plane-waves formalisms, the scheme has been tested for proton-transfer reactions in the cluster and the condensed phase and projected density of states of carbon monoxide adsorbed on platinum surface. With the computational scaling of the embedding potential optimization similar to that of hybrid density functional theory with a significantly reduced prefactor, the method allows for large-scale applications to extended systems.
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Affiliation(s)
- Vladimir V Rybkin
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, Zürich 8057, Switzerland
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20
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Xu J, Cao XM, Hu P. Accelerating Metadynamics-Based Free-Energy Calculations with Adaptive Machine Learning Potentials. J Chem Theory Comput 2021; 17:4465-4476. [PMID: 34100605 DOI: 10.1021/acs.jctc.1c00261] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
There is an increasing demand for free-energy calculations using ab initio molecular dynamics these days. Metadynamics (MetaD) is frequently utilized to reconstruct the free-energy surface, but it is often computationally intractable for the first-principles calculations. Machine learning potentials (MLPs) have become popular alternatives. However, the training could be a long and arduous process before using them in practical applications. To accelerate MetaD use with MLPs for the free-energy calculation in an easy manner, we propose the adaptive machine learning potential-accelerated metadynamics (AMLP-MetaD). In this method, the MLP in the form of a Gaussian approximation potential (GAP) can adapt itself based on its uncertainty estimation, which decides whether to accept the model prediction or recalculate it with a reference method (usually density functional theory) for further training during the MetaD simulation. We demonstrate that the free-energy landscape similar to the ab initio one can be obtained using AMLP-MetaD with a 10-time speedup. Moreover, the quality of the free-energy results can be deeply improved using Δ-MLP, which is the GAP-corrected density functional tight binding in our case. We exemplify this novel method with two model systems, CO adsorption on the Pt13 cluster and the Pt(111) surface, which are of vital importance in heterogeneous catalysis. The successful application in these two tests highlights that our proposed method can be used in both cluster and periodic systems and for up to two collective variables.
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Affiliation(s)
- Jiayan Xu
- School of Chemistry and Chemical Engineering, Queen's University Belfast, Belfast BT9 5AG, U.K
| | - Xiao-Ming Cao
- Key Laboratory for Advanced Materials, Centre for Computational Chemistry and Research Institute of Industrial Catalysis, School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
| | - P Hu
- School of Chemistry and Chemical Engineering, Queen's University Belfast, Belfast BT9 5AG, U.K
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21
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Casier B, Chagas da Silva M, Badawi M, Pascale F, Bučko T, Lebègue S, Rocca D. Hybrid localized graph kernel for machine learning energy-related properties of molecules and solids. J Comput Chem 2021; 42:1390-1401. [PMID: 34009668 DOI: 10.1002/jcc.26550] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 04/07/2021] [Accepted: 04/21/2021] [Indexed: 11/10/2022]
Abstract
Nowadays, the coupling of electronic structure and machine learning techniques serves as a powerful tool to predict chemical and physical properties of a broad range of systems. With the aim of improving the accuracy of predictions, a large number of representations for molecules and solids for machine learning applications has been developed. In this work we propose a novel descriptor based on the notion of molecular graph. While graphs are largely employed in classification problems in cheminformatics or bioinformatics, they are not often used in regression problem, especially of energy-related properties. Our method is based on a local decomposition of atomic environments and on the hybridization of two kernel functions: a graph kernel contribution that describes the chemical pattern and a Coulomb label contribution that encodes finer details of the local geometry. The accuracy of this new kernel method in energy predictions of molecular and condensed phase systems is demonstrated by considering the popular QM7 and BA10 datasets. These examples show that the hybrid localized graph kernel outperforms traditional approaches such as, for example, the smooth overlap of atomic positions and the Coulomb matrices.
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Affiliation(s)
- Bastien Casier
- Université de Lorraine and CNRS, LPCT, UMR 7019, F-54000 Nancy, France
| | | | - Michael Badawi
- Université de Lorraine and CNRS, LPCT, UMR 7019, F-54000 Nancy, France
| | | | - Tomáš Bučko
- Department of Physical and Theoretical Chemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia.,Institute of Inorganic Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Sébastien Lebègue
- Université de Lorraine and CNRS, LPCT, UMR 7019, F-54000 Nancy, France
| | - Dario Rocca
- Université de Lorraine and CNRS, LPCT, UMR 7019, F-54000 Nancy, France
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22
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Piaggi PM, Panagiotopoulos AZ, Debenedetti PG, Car R. Phase Equilibrium of Water with Hexagonal and Cubic Ice Using the SCAN Functional. J Chem Theory Comput 2021; 17:3065-3077. [PMID: 33835819 DOI: 10.1021/acs.jctc.1c00041] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Machine learning models are rapidly becoming widely used to simulate complex physicochemical phenomena with ab initio accuracy. Here, we use one such model as well as direct density functional theory (DFT) calculations to investigate the phase equilibrium of water, hexagonal ice (Ih), and cubic ice (Ic), with an eye toward studying ice nucleation. The machine learning model is based on deep neural networks and has been trained on DFT data obtained using the SCAN exchange and correlation functional. We use this model to drive enhanced sampling simulations aimed at calculating a number of complex properties that are out of reach of DFT-driven simulations and then employ an appropriate reweighting procedure to compute the corresponding properties for the SCAN functional. This approach allows us to calculate the melting temperature of both ice polymorphs, the driving force for nucleation, the heat of fusion, the densities at the melting temperature, the relative stability of ices Ih and Ic, and other properties. We find a correct qualitative prediction of all properties of interest. In some cases, quantitative agreement with experiment is better than for state-of-the-art semiempirical potentials for water. Our results also show that SCAN correctly predicts that ice Ih is more stable than ice Ic.
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Affiliation(s)
- Pablo M Piaggi
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Athanassios Z Panagiotopoulos
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States.,Princeton Institute for the Science and Technology of Materials, Princeton University, Princeton, New Jersey 08544, United States
| | - Pablo G Debenedetti
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States.,Princeton Institute for the Science and Technology of Materials, Princeton University, Princeton, New Jersey 08544, United States
| | - Roberto Car
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States.,Princeton Institute for the Science and Technology of Materials, Princeton University, Princeton, New Jersey 08544, United States.,Department of Physics, Princeton University, Princeton, New Jersey 08544, United States.,Program in Applied and Computational Mathematics, Princeton University, Princeton, New Jersey 08544, United States
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23
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Gešvandtnerová M, Rocca D, Bučko T. Methanol carbonylation over acid mordenite: Insights from ab initio molecular dynamics and machine learning thermodynamic perturbation theory. J Catal 2021. [DOI: 10.1016/j.jcat.2021.02.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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24
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Rey J, Bignaud C, Raybaud P, Bučko T, Chizallet C. Dynamic Features of Transition States for β-Scission Reactions of Alkenes over Acid Zeolites Revealed by AIMD Simulations. Angew Chem Int Ed Engl 2020; 59:18938-18942. [PMID: 32568440 DOI: 10.1002/anie.202006065] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 06/08/2020] [Indexed: 11/11/2022]
Abstract
Zeolite-catalyzed alkene cracking is key to optimize the size of hydrocarbons. The nature and stability of intermediates and transition states (TS) are, however, still debated. We combine transition path sampling and blue moon ensemble density functional theory simulations to unravel the behavior of C7 alkenes in CHA zeolite. Free energy profiles are determined, linking π-complexes, alkoxides and carbenium ions, for B1 (secondary to tertiary) and B2 (tertiary to secondary) β-scissions. B1 is found to be easier than B2 . The TS for B1 occurs at the breaking of the C-C bond, while for B2 it is the proton transfer from propenium to the zeolite. We highlight the dynamic behaviors of the various intermediates along both pathways, which reduce activation energies with respect to those previously evaluated by static approaches. We finally revisit the ranking of isomerization and cracking rate constants, which are crucial for future kinetic studies.
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Affiliation(s)
- Jérôme Rey
- IFP Energies nouvelles, Rond-Point de l'échangeur de Solaize, BP3, 69360, Solaize, France
| | - Charles Bignaud
- IFP Energies nouvelles, Rond-Point de l'échangeur de Solaize, BP3, 69360, Solaize, France.,Département de chimie, École normale supérieure, PSL University, 75005, Paris, France
| | - Pascal Raybaud
- IFP Energies nouvelles, Rond-Point de l'échangeur de Solaize, BP3, 69360, Solaize, France
| | - Tomáš Bučko
- Department of Physical and Theoretical Chemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 84215, Bratislava, Slovakia.,Institute of Inorganic Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 84236, Bratislava, Slovakia
| | - Céline Chizallet
- IFP Energies nouvelles, Rond-Point de l'échangeur de Solaize, BP3, 69360, Solaize, France
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25
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Jablonka K, Ongari D, Moosavi SM, Smit B. Big-Data Science in Porous Materials: Materials Genomics and Machine Learning. Chem Rev 2020; 120:8066-8129. [PMID: 32520531 PMCID: PMC7453404 DOI: 10.1021/acs.chemrev.0c00004] [Citation(s) in RCA: 158] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Indexed: 12/16/2022]
Abstract
By combining metal nodes with organic linkers we can potentially synthesize millions of possible metal-organic frameworks (MOFs). The fact that we have so many materials opens many exciting avenues but also create new challenges. We simply have too many materials to be processed using conventional, brute force, methods. In this review, we show that having so many materials allows us to use big-data methods as a powerful technique to study these materials and to discover complex correlations. The first part of the review gives an introduction to the principles of big-data science. We show how to select appropriate training sets, survey approaches that are used to represent these materials in feature space, and review different learning architectures, as well as evaluation and interpretation strategies. In the second part, we review how the different approaches of machine learning have been applied to porous materials. In particular, we discuss applications in the field of gas storage and separation, the stability of these materials, their electronic properties, and their synthesis. Given the increasing interest of the scientific community in machine learning, we expect this list to rapidly expand in the coming years.
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Affiliation(s)
- Kevin
Maik Jablonka
- Laboratory of Molecular Simulation
(LSMO), Institut des Sciences et Ingénierie Chimiques (ISIC), École Polytechnique Fédérale
de Lausanne (EPFL), Sion, Switzerland
| | - Daniele Ongari
- Laboratory of Molecular Simulation
(LSMO), Institut des Sciences et Ingénierie Chimiques (ISIC), École Polytechnique Fédérale
de Lausanne (EPFL), Sion, Switzerland
| | - Seyed Mohamad Moosavi
- Laboratory of Molecular Simulation
(LSMO), Institut des Sciences et Ingénierie Chimiques (ISIC), École Polytechnique Fédérale
de Lausanne (EPFL), Sion, Switzerland
| | - Berend Smit
- Laboratory of Molecular Simulation
(LSMO), Institut des Sciences et Ingénierie Chimiques (ISIC), École Polytechnique Fédérale
de Lausanne (EPFL), Sion, Switzerland
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26
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Rey J, Bignaud C, Raybaud P, Bučko T, Chizallet C. Dynamic Features of Transition States for β‐Scission Reactions of Alkenes over Acid Zeolites Revealed by AIMD Simulations. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202006065] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jérôme Rey
- IFP Energies nouvelles Rond-Point de l'échangeur de Solaize, BP3 69360 Solaize France
| | - Charles Bignaud
- IFP Energies nouvelles Rond-Point de l'échangeur de Solaize, BP3 69360 Solaize France
- Département de chimie École normale supérieure PSL University 75005 Paris France
| | - Pascal Raybaud
- IFP Energies nouvelles Rond-Point de l'échangeur de Solaize, BP3 69360 Solaize France
| | - Tomáš Bučko
- Department of Physical and Theoretical Chemistry Faculty of Natural Sciences Comenius University in Bratislava Ilkovičova 6 84215 Bratislava Slovakia
- Institute of Inorganic Chemistry Slovak Academy of Sciences Dúbravská cesta 9 84236 Bratislava Slovakia
| | - Céline Chizallet
- IFP Energies nouvelles Rond-Point de l'échangeur de Solaize, BP3 69360 Solaize France
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27
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Semmeq A, Badawi M, Hasnaoui A, Ouaskit S, Monari A. DNA Nucleobase under Ionizing Radiation: Unexpected Proton Transfer by Thymine Cation in Water Nanodroplets. Chemistry 2020; 26:11340-11344. [PMID: 32511805 DOI: 10.1002/chem.202002025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/04/2020] [Indexed: 11/07/2022]
Abstract
The effect of ionizing radiation on DNA constituents is a widely studied fundamental process using experimental and computational techniques. In particular, radiation effects on nucleobases are usually tackled by mass spectrometry in which the nucleobase is embedded in a water nanodroplet. Here, we present a multiscale theoretical study revealing the effects and the dynamics of water droplets towards neutral and ionized thymine. In particular, by using both hybrid quantum mechanics/molecular mechanics and full ab initio molecular dynamics, we reveal an unexpected proton transfer from thymine cation to a nearby water molecule. This leads to the formation of a neutral radical thymine and a Zundel structure, while the hydrated proton localizes at the interface between the deprotonated thymine and the water droplet. This observation opens entirely novel perspectives concerning the reactivity and further fragmentation of ionized nucleobases.
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Affiliation(s)
- Abderrahmane Semmeq
- Université de Lorraine and CNRS, LPCT UMR 7019, 54000, Nancy, France.,Laboratoire de Physique de la Matière Condensée LPMC Faculté des, Sciences Ben M'sik, University Hassan II of Casablanca, BP 7955 Av. Driss El Harti, Sidi Othmane, 20000, Casablanca, Morocco
| | - Michael Badawi
- Université de Lorraine and CNRS, LPCT UMR 7019, 54000, Nancy, France
| | - Abdellatif Hasnaoui
- LS3M, Faculté Polydisicplinaire-Khouribga, University Sultan Moulay Slimane of Beni Mellal, B.P 145, 25000, Khouribga, Morocco
| | - Said Ouaskit
- Laboratoire de Physique de la Matière Condensée LPMC Faculté des, Sciences Ben M'sik, University Hassan II of Casablanca, BP 7955 Av. Driss El Harti, Sidi Othmane, 20000, Casablanca, Morocco
| | - Antonio Monari
- Université de Lorraine and CNRS, LPCT UMR 7019, 54000, Nancy, France
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28
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Bučko T, Gešvandtnerová M, Rocca D. Ab Initio Calculations of Free Energy of Activation at Multiple Electronic Structure Levels Made Affordable: An Effective Combination of Perturbation Theory and Machine Learning. J Chem Theory Comput 2020; 16:6049-6060. [DOI: 10.1021/acs.jctc.0c00486] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tomáš Bučko
- Department of Physical and Theoretical Chemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, SK-84215 Bratislava, Slovakia
- Institute of Inorganic Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, SK-84236 Bratislava, Slovakia
| | - Monika Gešvandtnerová
- Department of Physical and Theoretical Chemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, SK-84215 Bratislava, Slovakia
| | - Dario Rocca
- Université de Lorraine and CNRS, LPCT UMR 7019, F-54000 Nancy, France
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29
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Foucaud Y, Filippov L, Filippova I, Badawi M. The Challenge of Tungsten Skarn Processing by Froth Flotation: A Review. Front Chem 2020; 8:230. [PMID: 32373577 PMCID: PMC7179254 DOI: 10.3389/fchem.2020.00230] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 03/10/2020] [Indexed: 11/13/2022] Open
Abstract
Recently, tungsten has drawn worldwide attention considering its high supply risk and economic importance in the modern society. Skarns represent one of the most important types of tungsten deposits in terms of reserves. They contain fine-grained scheelite (CaWO4) associated with complex gangue minerals, i.e., minerals that display similar properties, particularly surface properties, compared to scheelite. Consistently, the froth flotation of scheelite still remains, in the twenty first century, a strong scientific, industrial, and technical challenge. Various reagents suitable for scheelite flotation (collectors and depressants, mostly) are reviewed in the present work, with a strong focus on the separation of scheelite from calcium salts, namely, fluorite, apatite, and calcite, which generally represent significant amounts in tungsten skarns. Albeit some reagents allow increasing significantly the selectivity regarding a mineral, most reagents fail in providing a good global selectivity in favor of scheelite. Overall, the greenest, most efficient, and cheapest method for scheelite flotation is to use fatty acids as collectors with sodium silicate as depressant, although this solution suffers from a crucial lack of selectivity regarding the above-mentioned calcium salts. Therefore, the use of reagent combinations, commonly displaying synergistic effects, is highly recommended to achieve a selective flotation of scheelite from the calcium salts as well as from calcium silicates.
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Affiliation(s)
- Yann Foucaud
- Université de Lorraine, CNRS, GeoRessources, Nancy, France
| | - Lev Filippov
- Université de Lorraine, CNRS, GeoRessources, Nancy, France.,National University of Science and Technology MISIS, Moscow, Russia
| | - Inna Filippova
- Université de Lorraine, CNRS, GeoRessources, Nancy, France
| | - Michael Badawi
- Université de Lorraine, CNRS, Laboratoire de Physique et Chimie Théoriques, Nancy, France
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30
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Abstract
As the quantum chemistry (QC) community embraces machine learning (ML), the number of new methods and applications based on the combination of QC and ML is surging. In this Perspective, a view of the current state of affairs in this new and exciting research field is offered, challenges of using machine learning in quantum chemistry applications are described, and potential future developments are outlined. Specifically, examples of how machine learning is used to improve the accuracy and accelerate quantum chemical research are shown. Generalization and classification of existing techniques are provided to ease the navigation in the sea of literature and to guide researchers entering the field. The emphasis of this Perspective is on supervised machine learning.
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Affiliation(s)
- Pavlo O Dral
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Department of Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
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Klimeš J, Tew DP. Efficient and accurate description of adsorption in zeolites. J Chem Phys 2019; 151:234108. [PMID: 31864262 DOI: 10.1063/1.5123425] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Accurate theoretical methods are needed to correctly describe adsorption on solid surfaces or in porous materials. The random phase approximation (RPA) with singles corrections scheme and the second order Møller-Plesset perturbation theory (MP2) are two schemes, which offer high accuracy at affordable computational cost. However, there is little knowledge about their applicability and reliability for different adsorbates and surfaces. Here, we calculate adsorption energies of seven different molecules in zeolite chabazite to show that RPA with singles corrections is superior to MP2, not only in terms of accuracy but also in terms of computer time. Therefore, RPA with singles is a suitable scheme for obtaining highly accurate adsorption energies in porous materials and similar systems.
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Affiliation(s)
- Jiří Klimeš
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, CZ-12116 Prague 2, Czech Republic
| | - David P Tew
- Max-Planck-Institut für Festkörperforschung, Heisenbergstraße 1, 70569 Stuttgart, Germany
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