1
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Blöndal K, Badger K, Sargsyan K, Bross DH, Ruscic B, Goldsmith CF. Importance sampling within configuration space integration for adsorbate thermophysical properties: a case study for CH 3/Ni(111). Phys Chem Chem Phys 2024; 26:17265-17273. [PMID: 38856369 DOI: 10.1039/d4cp01197j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
A new strategy is presented for computing anharmonic partition functions for the motion of adsorbates relative to a catalytic surface. Importance sampling is compared with conventional Monte Carlo. The importance sampling is significantly more efficient. This new approach is applied to CH3* on Ni(111) as a test case. The motion of methyl relative to the nickel surface is found to be anharmonic, with significantly higher entropy compared to the standard harmonic oscillator model. The new method is freely available as part of the Minima-Preserving Neural Network within the ADTHERM package.
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Affiliation(s)
- Katrín Blöndal
- Chemical Engineering Group, School of Engineering, Brown University, Providence, RI 02912, USA.
| | - Kirk Badger
- Chemical Engineering Group, School of Engineering, Brown University, Providence, RI 02912, USA.
| | | | - David H Bross
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Branko Ruscic
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - C Franklin Goldsmith
- Chemical Engineering Group, School of Engineering, Brown University, Providence, RI 02912, USA.
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2
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Crossley-Lewis J, Dunn J, Hickman IF, Jackson F, Sunley GJ, Buda C, Mulholland AJ, Allan NL. Multilevel quantum mechanical calculations show the role of promoter molecules in the dehydration of methanol to dimethyl ether in H-ZSM-5. Phys Chem Chem Phys 2024; 26:16693-16707. [PMID: 38809246 DOI: 10.1039/d3cp05987a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
Methyl carboxylate esters promote the formation of dimethyl ether (DME) from the dehydration of methanol in H-ZSM-5 zeolite. We employ a multilevel quantum method to explore the possible associative and dissociative mechanisms in the presence, and absence, of six methyl ester promoters. This hybrid method combines density functional theory, with dispersion corrections (DFT-D3), for the full periodic system, with second-order Møller-Plesset perturbation theory (MP2) for small clusters representing the reaction site, and coupled cluster with single, double, and perturbative triple substitution (CCSD(T)) for the reacting molecules. The calculated adsorption enthalpy of methanol, and reaction enthalpies of the dehydration of methanol to DME within H-ZSM-5, agree with experiment to within chemical accuracy (∼4 kJ mol-1). For the promoters, a reaction pathway via an associative mechanism gives lower overall reaction enthalpies and barriers compared to the reaction with methanol only. Each stage of this mechanism is explored and related to experimental data. We provide evidence that suggests the promoter's adsorption to the Brønsted acid site is the most important factor dictating its efficiency.
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Affiliation(s)
- Joe Crossley-Lewis
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
| | - Josh Dunn
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
| | - Isabel F Hickman
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
| | - Fiona Jackson
- Applied Sciences, bp Innovation and Engineering, BP plc, Saltend, Hull, HU12 8DS, UK
| | - Glenn J Sunley
- Applied Sciences, bp Innovation and Engineering, BP plc, Saltend, Hull, HU12 8DS, UK
| | - Corneliu Buda
- Applied Sciences, bp Innovation and Engineering, BP plc, 30 South Wacker Drive, Chicago, IL 60606, USA
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
| | - Neil L Allan
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
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3
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Hoffman AJ, Temmerman W, Campbell E, Damin AA, Lezcano-Gonzalez I, Beale AM, Bordiga S, Hofkens J, Van Speybroeck V. A Critical Assessment on Calculating Vibrational Spectra in Nanostructured Materials. J Chem Theory Comput 2024; 20:513-531. [PMID: 38157404 PMCID: PMC10809426 DOI: 10.1021/acs.jctc.3c00942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 11/30/2023] [Accepted: 12/05/2023] [Indexed: 01/03/2024]
Abstract
Vibrational spectroscopy is an omnipresent spectroscopic technique to characterize functional nanostructured materials such as zeolites, metal-organic frameworks (MOFs), and metal-halide perovskites (MHPs). The resulting experimental spectra are usually complex, with both low-frequency framework modes and high-frequency functional group vibrations. Therefore, theoretically calculated spectra are often an essential element to elucidate the vibrational fingerprint. In principle, there are two possible approaches to calculate vibrational spectra: (i) a static approach that approximates the potential energy surface (PES) as a set of independent harmonic oscillators and (ii) a dynamic approach that explicitly samples the PES around equilibrium by integrating Newton's equations of motions. The dynamic approach considers anharmonic and temperature effects and provides a more genuine representation of materials at true operating conditions; however, such simulations come at a substantially increased computational cost. This is certainly true when forces and energy evaluations are performed at the quantum mechanical level. Molecular dynamics (MD) techniques have become more established within the field of computational chemistry. Yet, for the prediction of infrared (IR) and Raman spectra of nanostructured materials, their usage has been less explored and remain restricted to some isolated successes. Therefore, it is currently not a priori clear which methodology should be used to accurately predict vibrational spectra for a given system. A comprehensive comparative study between various theoretical methods and experimental spectra for a broad set of nanostructured materials is so far lacking. To fill this gap, we herein present a concise overview on which methodology is suited to accurately predict vibrational spectra for a broad range of nanostructured materials and formulate a series of theoretical guidelines to this purpose. To this end, four different case studies are considered, each treating a particular material aspect, namely breathing in flexible MOFs, characterization of defects in the rigid MOF UiO-66, anharmonic vibrations in the metal-halide perovskite CsPbBr3, and guest adsorption on the pores of the zeolite H-SSZ-13. For all four materials, in their guest- and defect-free state and at sufficiently low temperatures, both the static and dynamic approach yield qualitatively similar spectra in agreement with experimental results. When the temperature is increased, the harmonic approximation starts to fail for CsPbBr3 due to the presence of anharmonic phonon modes. Also, the spectroscopic fingerprints of defects and guest species are insufficiently well predicted by a simple harmonic model. Both phenomena flatten the potential energy surface (PES), which facilitates the transitions between metastable states, necessitating dynamic sampling. On the basis of the four case studies treated in this Review, we can propose the following theoretical guidelines to simulate accurate vibrational spectra of functional solid-state materials: (i) For nanostructured crystalline framework materials at low temperature, insights into the lattice dynamics can be obtained using a static approach relying on a few points on the PES and an independent set of harmonic oscillators. (ii) When the material is evaluated at higher temperatures or when additional complexity enters the system, e.g., strong anharmonicity, defects, or guest species, the harmonic regime breaks down and dynamic sampling is required for a correct prediction of the phonon spectrum. These guidelines and their illustrations for prototype material classes can help experimental and theoretical researchers to enhance the knowledge obtained from a lattice dynamics study.
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Affiliation(s)
| | - Wim Temmerman
- Center
for Molecular Modeling, Ghent University, 9000 Ghent, Belgium
| | - Emma Campbell
- Cardiff
Catalysis Institute, Cardiff University, Cardiff CF10 3AT, United Kingdom
- Research
Complex at Harwell, Didcot OX11 0FA, United
Kingdom
| | | | - Ines Lezcano-Gonzalez
- Research
Complex at Harwell, Didcot OX11 0FA, United
Kingdom
- Department
of Chemistry, University College London, London WC1E 6BT, United Kingdom
| | - Andrew M. Beale
- Research
Complex at Harwell, Didcot OX11 0FA, United
Kingdom
- Department
of Chemistry, University College London, London WC1E 6BT, United Kingdom
| | - Silvia Bordiga
- Department
of Chemistry, University of Turin, 10124 Turin, Italy
| | - Johan Hofkens
- Department
of Chemistry, KU Leuven, 3000 Leuven, Belgium
- Max Planck
Institute for Polymer Research, 55128 Mainz, Germany
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4
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Hutton DJ, Göltl F. Free and internal energies for the adsorption of short alkanes into the zeolite SSZ-13 from ab initio molecular dynamics simulations. Phys Chem Chem Phys 2023; 25:26604-26612. [PMID: 37753843 DOI: 10.1039/d3cp02523c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2023]
Abstract
Electronic structure calculations have become a valuable tool in understanding chemical reactions of hydrocarbons in zeolite pores. However, commonly applied approaches to calculate free energies based on static electronic structure calculations significantly overestimate the entropic penalty for molecular adsorption into zeolite pores. Here, we use ab initio molecular dynamics (AIMD) simulations to model the adsorption of methane, ethane, and propane to purely siliceous and protonated SSZ-13. In our analyses we focus on the internal and Helmholtz free energies of adsorption of each molecule and compare our results to various approaches for the calculation of free energies based on static calculations. We find that only an approach that retains two thirds of the translational entropy of the adsorbate upon adsorption compares favorably with AIMD simulations. However, comparison to experimental measurements of Gibbs free energies of adsorption reported in the literature implies that we might not have captured the full complexity of alkane adsorption in our model. We expect that results in this work will help to develop a better understanding of alkane adsorption in zeolites, and that the provided data will serve as a benchmark for free energy calculations of alkane adsorption in zeolites in the future.
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Affiliation(s)
- Daniel J Hutton
- Department of Biosystem Engineering, The University of Arizona, 1177 E 4th Street, Tucson, AZ, USA.
| | - Florian Göltl
- Department of Biosystem Engineering, The University of Arizona, 1177 E 4th Street, Tucson, AZ, USA.
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5
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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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Beynon O, Owens A, Carbogno C, Logsdail AJ. Evaluating the Role of Anharmonic Vibrations in Zeolite β Materials. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2023; 127:16030-16040. [PMID: 37609380 PMCID: PMC10440812 DOI: 10.1021/acs.jpcc.3c02863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 07/16/2023] [Indexed: 08/24/2023]
Abstract
The characterization of zeolitic materials is often facilitated by spectroscopic analysis of vibrations, which informs about the bonding character of the substrate and any adsorbents. Computational simulations aid the interpretation of the spectra but often ignore anharmonic effects that can affect the spectral characteristics significantly. Here, the impact of anharmonicity is demonstrated with a combination of dynamical and static simulations applied to the structures formed during the synthesis of Sn-BEA via solid-state incorporation (SSI): the initial siliceous BEA (Si-β), aluminosilicate BEA (H-β), dealuminated BEA (deAl-β), and Sn-BEA (Sn-β). Heteroatom and defect-containing BEA are shown to have strong anharmonic vibrational contributions, with atomic and elemental resolution highlighting particularly the prevalence for H atoms (H-β, deAl-β) as well as localization to heteroatoms at defect sites. We simulate the vibrational spectra of BEA accounting for anharmonic contributions and observe an improved agreement with experimental data compared to harmonic methods, particularly at wavenumbers below 1500 cm-1. The results demonstrate the importance of incorporating anharmonic effects in simulations of vibrational spectra, with consequences toward future characterization and application of zeolitic materials.
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Affiliation(s)
- Owain
T. Beynon
- Cardiff
Catalysis Institute, Cardiff University, Park Place, Cardiff CF10 3AT, Wales, U.K.
| | - Alun Owens
- Cardiff
Catalysis Institute, Cardiff University, Park Place, Cardiff CF10 3AT, Wales, U.K.
| | - Christian Carbogno
- The
NOMAD Laboratory at the FHI of the Max-Planck-Gesellschaft and IRIS-Adlershof
of the Humboldt-Universität zu Berlin, Faradayweg 4-6, 14195 Berlin, Germany
| | - Andrew J. Logsdail
- Cardiff
Catalysis Institute, Cardiff University, Park Place, Cardiff CF10 3AT, Wales, U.K.
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7
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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 DOI: 10.1098/rsta.2022.0239] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [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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8
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Bunting RJ, Wodaczek F, Torabi T, Cheng B. Reactivity of Single-Atom Alloy Nanoparticles: Modeling the Dehydrogenation of Propane. J Am Chem Soc 2023. [PMID: 37390457 DOI: 10.1021/jacs.3c04030] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/02/2023]
Abstract
Physical catalysts often have multiple sites where reactions can take place. One prominent example is single-atom alloys, where the reactive dopant atoms can preferentially locate in the bulk or at different sites on the surface of the nanoparticle. However, ab initio modeling of catalysts usually only considers one site of the catalyst, neglecting the effects of multiple sites. Here, nanoparticles of copper doped with single-atom rhodium or palladium are modeled for the dehydrogenation of propane. Single-atom alloy nanoparticles are simulated at 400-600 K, using machine learning potentials trained on density functional theory calculations, and then the occupation of different single-atom active sites is identified using a similarity kernel. Further, the turnover frequency for all possible sites is calculated for propane dehydrogenation to propene through microkinetic modeling using density functional theory calculations. The total turnover frequencies of the whole nanoparticle are then described from both the population and the individual turnover frequency of each site. Under operating conditions, rhodium as a dopant is found to almost exclusively occupy (111) surface sites while palladium as a dopant occupies a greater variety of facets. Undercoordinated dopant surface sites are found to tend to be more reactive for propane dehydrogenation compared to the (111) surface. It is found that considering the dynamics of the single-atom alloy nanoparticle has a profound effect on the calculated catalytic activity of single-atom alloys by several orders of magnitude.
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Affiliation(s)
- Rhys J Bunting
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
| | - Felix Wodaczek
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
| | - Tina Torabi
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
| | - Bingqing Cheng
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
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9
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Amsler J, Plessow PN, Studt F, Bučko T. Anharmonic Correction to Free Energy Barriers from DFT-Based Molecular Dynamics Using Constrained Thermodynamic Integration. J Chem Theory Comput 2023; 19:2455-2468. [PMID: 37043693 DOI: 10.1021/acs.jctc.3c00169] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
For the calculation of anharmonic contributions to free energy barriers, constrained thermodynamic λ-path integration (λ-TI) from a harmonic reference force field to density functional theory is presented as an alternative to the established Blue Moon ensemble method (ξ-TI), in which free energy gradients along the reaction coordinate ξ are integrated. With good agreement in all cases, the λ-TI method is benchmarked against the ξ-TI method for several reactions, including the internal CH3 group rotation in ethane, a nucleophilic substitution of CH3Cl, a retro-Diels-Alder reaction, and a proton transfer in zeolite H-SSZ-13. An advantage of λ-TI is that one can use virtually any reference state to compute anharmonic contributions to reaction free energies or free energy barriers. This is particularly relevant for catalysis, where it is now possible to compute anharmonic corrections to the free energy of a transition state relative to any reference, for example, the most stable state of the active site and the reactants in the gas phase. This is in contrast to ξ-TI, where free energy barriers can only be computed relative to an initial state with all reactants coadsorbed. Finally, the Bennett acceptance ratio method combined with λ-TI is demonstrated to reduce the number of required integration grid points with tolerable accuracy, favoring thus λ-TI over ξ-TI in terms of computational efficiency.
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Affiliation(s)
- Jonas Amsler
- Institute of Catalysis Research and Technology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Philipp N Plessow
- Institute of Catalysis Research and Technology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Felix Studt
- Institute of Catalysis Research and Technology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
- Institute for Chemical Technology and Polymer Chemistry, Karlsruhe Institute of Technology, Kaiserstr. 12, 76131 Karlsruhe, Germany
| | - 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
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10
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Kurdziel SJ, Vlachos DG. Transition-state correlations for predicting thermochemistry of adsorbates and surface reactions. Phys Chem Chem Phys 2023; 25:8412-8423. [PMID: 36912605 DOI: 10.1039/d2cp04425k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
Abstract
Estimating thermochemical properties from linear correlations may provide a pathway to circumvent expensive density functional theory (DFT) calculations for quantities such as pre-exponentials and temperature corrections to DFT energies. Here, we construct thermochemical scaling relations between C1-C6n-alkanes in the gas phase and adsorbed alkyl chains extending from several transition metal surfaces, and examine changes in the slope and fit between metals and adsorption sites. We subsequently add -OH, -NH2, CO, and CC functional groups to the C1-C6 molecules and demonstrate strong linear correlations for thermochemistry across all species. We broaden the correlations to incorporate transition states of C1-C6n-alkane dehydrogenation reactions, where thermochemistry for computationally prohibitive transition-state calculations can be quickly assessed. Additionally, we rationalize the linearity of thermochemical correlations based on the composition of the homologous series and theoretical assessments. As an application of the correlations, we estimate pre-exponentials for elementary surface reactions of ethane and propane hydrogenolysis on Ru(0001), which is of relevance to plastic hydrogenolysis. Depending on kinetically important steps, entropic contributions may be necessary to include in certain reaction mechanisms; in contrasting examples, entropies are found to be relatively insignificant for ethane hydrogenolysis but pertinent for propane hydrogenolysis.
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Affiliation(s)
- Sophia J Kurdziel
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, DE, 19716, USA.
| | - Dionisios G Vlachos
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, DE, 19716, USA.
- Catalysis Center for Energy Innovation, RAPID Manufacturing Institute, Delaware Energy Institute (DEI), University of Delaware, 221 Academy Street, Newark, DE, 19716, USA
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11
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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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12
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Rybicki M, Sillar K, Sauer J. Dual-Site Model for Ab Initio Calculations of Gibbs Free Energies and Enthalpies of Adsorption: Methane in Zeolite Mobile Five (H-MFI). J Phys Chem Lett 2022; 13:11595-11600. [PMID: 36480747 DOI: 10.1021/acs.jpclett.2c03302] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Quantum chemical hybrid MP2:PBE+D2 calculations in combination with molecular statistics are employed to calculate enthalpies and Gibbs free energies of adsorption for CH4 at Brønsted acid sites [bridging Si-O(H)-Al groups] and silica wall sites (Si-O-Si) of the proton form of zeolite MFI (H-ZSM-5) and its purely siliceous analogue Silicalite-1. A Langmuir model is adopted to calculate the amounts of CH4 adsorbed at each type of site from the Gibbs free energies. The combination of these results according to the ratio of silica wall sites and Brønsted acid sites in the sample yields adsorption isotherms for zeolites with different Si/Al ratios. The zero-coverage isosteric heats of adsorption, calculated as thermal averages of the adsorption enthalpies of the individual sites, vary between 20.2 kJ/mol for the pore wall site and 29.2 kJ/mol for the acid site and agree well within ±1 kJ/mol with experimental results.
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Affiliation(s)
- Marcin Rybicki
- Institute of Chemistry, Humboldt-Universitaät zu Berlin, Unter den Linden 6, 10099Berlin, Germany
| | - Kaido Sillar
- Institute of Chemistry, Humboldt-Universitaät zu Berlin, Unter den Linden 6, 10099Berlin, Germany
- University of Tartu, Institute of Chemistry, Ravila 14a, 50411Tartu, Estonia
| | - Joachim Sauer
- Institute of Chemistry, Humboldt-Universitaät zu Berlin, Unter den Linden 6, 10099Berlin, Germany
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13
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Blöndal K, Sargsyan K, Bross DH, Ruscic B, Goldsmith CF. Configuration Space Integration for Adsorbate Partition Functions: The Effect of Anharmonicity on the Thermophysical Properties of CO–Pt(111) and CH 3OH–Cu(111). ACS Catal 2022. [DOI: 10.1021/acscatal.2c04246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Katrín Blöndal
- Chemical Engineering Group, School of Engineering, Brown University, Providence, Rhode Island02912, United States
| | - Khachik Sargsyan
- Sandia National Laboratories, Livermore, California94550, United States
| | - David H. Bross
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois60439, United States
| | - Branko Ruscic
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois60439, United States
| | - C. Franklin Goldsmith
- Chemical Engineering Group, School of Engineering, Brown University, Providence, Rhode Island02912, United States
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14
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Rangarajan S, Tian H. Improving the predictive power of microkinetic models via machine learning. Curr Opin Chem Eng 2022. [DOI: 10.1016/j.coche.2022.100858] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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15
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Singh MB, Sharma R, Kumar D, Khanna P, Mansi, Khanna L, Kumar V, Kumari K, Gupta A, Chaudhary P, Kaushik N, Choi EH, Kaushik NK, Singh P. An understanding of coronavirus and exploring the molecular dynamics simulations to find promising candidates against the Mpro of nCoV to combat the COVID-19: A systematic review. J Infect Public Health 2022; 15:1326-1349. [PMID: 36288640 PMCID: PMC9579205 DOI: 10.1016/j.jiph.2022.10.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 10/08/2022] [Accepted: 10/12/2022] [Indexed: 11/10/2022] Open
Abstract
The first infection case of new coronavirus was reported at the end of 2019 and after then, the cases are reported in all nations across the world in a very short period. Further, the regular news of mutations in the virus has made life restricted with appropriate behavior. To date, a new strain (Omicron and its new subvariant Omicron XE) has brought fear amongst us due to a higher trajectory of increase in the number of cases. The researchers thus started giving attention to this viral infection and discovering drug-like candidates to cure the infections. Finding a drug for any viral infection is not an easy task and takes plenty of time. Therefore, computational chemistry/bioinformatics is followed to get promising molecules against viral infection. Molecular dynamics (MD) simulations are being explored to get drug candidates in a short period. The molecules are screened via molecular docking, which provides preliminary information which can be further verified by molecular dynamics (MD) simulations. To understand the change in structure, MD simulations generated several trajectories such as root mean square deviation (RMSD), root mean square fluctuation (RMSF), hydrogen bonding, and radius of gyration for the main protease (Mpro) of the new coronavirus (nCoV) in the presence of small molecules. Additionally, change in free energy for the formation of complex of Mpro of nCoV with the small molecule can be determined by applying molecular mechanics with generalized born and surface area solvation (MM-GBSA). Thus, the promising molecules can be further explored for clinical trials to combat coronavirus disease-19 (COVID-19).
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Affiliation(s)
- Madhur Babu Singh
- Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, New Delhi, India
| | - Ritika Sharma
- Department of Biochemistry, University of Delhi, New Delhi, India
| | - Durgesh Kumar
- Department of Chemistry, Maitreyi College, University of Delhi, Delhi, India
| | - Pankaj Khanna
- Department of Chemistry, Acharya Narendra Dev College, University of Delhi, New Delhi, India
| | - Mansi
- University School of Basic and Applied Sciences, Guru Gobind Singh Indraprastha University, New Delhi, India
| | - Leena Khanna
- University School of Basic and Applied Sciences, Guru Gobind Singh Indraprastha University, New Delhi, India
| | - Vinod Kumar
- Special Centre for Nanoscience (SCNS), Jawaharlal Nehru University, New Delhi, India
| | - Kamlesh Kumari
- Department of Zoology, University of Delhi, New Delhi, India
| | - Akanksha Gupta
- Department of Chemistry, Sri Venkateswara College, University of Delhi, New Delhi, India
| | - Preeti Chaudhary
- Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, New Delhi, India
| | - Neha Kaushik
- Department of Biotechnology, College of Engineering, The University of Suwon, Hwaseong-si 18323, Republic of Korea.
| | - Eun Ha Choi
- Plasma Bioscience Research Center, Department of Electrical and Biological Physics, Kwangwoon University, Seoul 01897, Republic of Korea
| | - Nagendra Kumar Kaushik
- Plasma Bioscience Research Center, Department of Electrical and Biological Physics, Kwangwoon University, Seoul 01897, Republic of Korea.
| | - Prashant Singh
- Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, New Delhi, India.
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16
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Li SC, Lin YC, Li YP. Comparative Analysis of Uncoupled Mode Approximations for Molecular Thermochemistry and Kinetics. J Chem Theory Comput 2022; 18:6866-6877. [PMID: 36269729 DOI: 10.1021/acs.jctc.2c00664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The accurate prediction of thermochemistry and kinetic parameters is an important task for reaction modeling. Unfortunately, the commonly used harmonic oscillator model is often not accurate enough due to the absence of anharmonic effects. In this work, we improve the representation of an anharmonic potential energy surface (PES) using uncoupled mode (UM) approximations, which model the full-dimensional PES as a sum of one-dimensional potentials of each mode. We systematically analyze different PES sampling schemes and coordinate systems for constructing the one-dimensional potentials, and benchmark the performance of UM methods on data sets of molecular thermochemistry and kinetic properties. The results show that the accuracy of the UM approach strongly depends on how the one-dimensional potentials are defined. If one-dimensional potentials are constructed by sampling along normal mode directions (UM-N) or along the directions that minimize intermode coupling (E- and E'-optimized), the accuracies of the predicted properties are not significantly improved compared to the harmonic oscillator model. However, significant improvements can be achieved by sampling the torsional modes separately from the vibrational modes (UM-T and UM-VT). In this work, three types of coordinate systems are examined, including redundant internal coordinates (RIC), hybrid internal coordinates (HIC), and translation-rotation-internal coordinates (TRIC). The HIC and TRIC coordinate systems can outperform RIC since transition state species may contain large-amplitude interfragmentary motions that regular internal coordinates can not describe adequately. Among all the methods we examined, the activation energies and pre-exponential factors calculated using UM-VT with either TRIC or HIC best agree with the reference values. Since UM-VT requires only a number of additional single point energy calculations for each independent mode, the scaling of computational costs of UM-VT is the same as that of the standard harmonic oscillator model, making UM-VT an appealing way of calculating the thermochemistry and kinetic properties for large-size systems.
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Affiliation(s)
- Shih-Cheng Li
- Department of Chemical Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan
| | - Yen-Chun Lin
- Department of Chemical Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan
| | - 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), Academia Sinica, No. 128, Sec. 2, Academia Road, Taipei 11529, Taiwan
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17
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Rybicki M, Sauer J. Rigid Body Approximation for the Anharmonic Description of Molecule-Surface Vibrations. J Chem Theory Comput 2022; 18:5618-5635. [PMID: 35913469 DOI: 10.1021/acs.jctc.2c00597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present an anharmonic approach for molecule-surface vibrations that employs rigid body coordinates, based on the Rodrigues rotation formula, to describe curvilinear displacements (rotations and translations) of the molecule along normal modes. These displacements are used to calculate energy data points from which one-dimensional polynomial potentials are fitted using cubic splines. In these potentials, for each of the six rigid body modes separately, one-dimensional Schrödinger equations are solved with harmonic oscillator or Fourier functions (for pure rotations) as basis sets. The anharmonic vibrational energies obtained are used to calculate partition functions and from them enthalpies, entropies, and Gibbs free energies of adsorption. Our numerical implementation has been successfully tested for Morse and cosine potentials with known analytical solutions. The methods have been applied to adsorption of CH4 on the hydroxyl group of the proton form of the chabazite zeolite (H-CHA), as well as to adsorption of CH4 and CO on the Mg2+ ions of the metal-organic framework (MOF) Mg2(dobdc). To obtain the best estimates for thermodynamic functions, we include the coupling between molecule-surface vibrations and intrasystem vibrations at the harmonic level. The calculated Gibbs free energies show that the coupling is small for CH4/H-CHA and CO/MOF (between -0.7 and +0.1 kJ/mol) but substantial for CH4/MOF (-3.4 kJ/mol). The predicted anharmonic effect on the Gibbs free energy of adsorption for CH4/H-CHA, CH4/MOF, and CO/MOF is -4.7, 0.3 ± 0.7, and -2.4 ± 0.6 kJ/mol, respectively, which results in +4.2, +0.9 ± 0.7, and -0.4 ± 0.6 kJ/mol, respectively, for the deviation from experiment. This is well within chemical accuracy limits (±4.2 kJ/mol) for the adsorption of CH4 and CO in the MOF. The larger deviation for CH4/H-CHA, at the edge of the chemical accuracy range, is most likely due to contributions from soft zeolite modes which are neglected in our approach.
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Affiliation(s)
- Marcin Rybicki
- Institut für Chemie, Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Joachim Sauer
- Institut für Chemie, Humboldt-Universität zu Berlin, 10117 Berlin, Germany.,Department of Physical and Macromolecular Chemistry/Charles University Center of Advanced Materials, Charles University, Hlavova 8, 128 43 Prague 2, Czech Republic
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18
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Abstract
Differences in entropies of competing transition states can direct kinetic selectivity. Understanding and modeling such entropy differences at the molecular level is complicated by the fact that entropy is statistical in nature; i.e., it depends on multiple vibrational states of transition structures, the existence of multiple dynamically accessible pathways past these transition structures, and contributions from multiple transition structures differing in conformation/configuration. The difficulties associated with modeling each of these contributors are discussed here, along with possible solutions, all with an eye toward the development of portable qualitative models of use to experimentalists aiming to design reactions that make use of entropy to control kinetic selectivity.
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Affiliation(s)
- Dean J Tantillo
- Department of Chemistry, University of California-Davis, 1 Shields Ave, Davis, California 95616, United States
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19
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Pineda M, Stamatakis M. Kinetic Monte Carlo simulations for heterogeneous catalysis: Fundamentals, current status, and challenges. J Chem Phys 2022; 156:120902. [DOI: 10.1063/5.0083251] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Kinetic Monte Carlo (KMC) simulations in combination with first-principles (1p)-based calculations are rapidly becoming the gold-standard computational framework for bridging the gap between the wide range of length scales and time scales over which heterogeneous catalysis unfolds. 1p-KMC simulations provide accurate insights into reactions over surfaces, a vital step toward the rational design of novel catalysts. In this Perspective, we briefly outline basic principles, computational challenges, successful applications, as well as future directions and opportunities of this promising and ever more popular kinetic modeling approach.
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Affiliation(s)
- M. Pineda
- Thomas Young Centre and Department of Chemical Engineering, University College London, Roberts Building, Torrington Place, London WC1E 7JE, United Kingdom
| | - M. Stamatakis
- Thomas Young Centre and Department of Chemical Engineering, University College London, Roberts Building, Torrington Place, London WC1E 7JE, United Kingdom
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20
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Piccini G, Lee MS, Yuk SF, Zhang D, Collinge G, Kollias L, Nguyen MT, Glezakou VA, Rousseau R. Ab initio molecular dynamics with enhanced sampling in heterogeneous catalysis. Catal Sci Technol 2022. [DOI: 10.1039/d1cy01329g] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Enhanced sampling ab initio simulations enable to study chemical phenomena in catalytic systems including thermal effects & anharmonicity, & collective dynamics describing enthalpic & entropic contributions, which can significantly impact on reaction free energy landscapes.
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Affiliation(s)
- GiovanniMaria Piccini
- Basic & Applied Molecular Foundations, Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
- Istituto Eulero, Università della Svizzera italiana, Via Giuseppe Buffi 13, Lugano, Ticino, Switzerland
| | - Mal-Soon Lee
- Basic & Applied Molecular Foundations, Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Simuck F. Yuk
- Basic & Applied Molecular Foundations, Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
| | - Difan Zhang
- Basic & Applied Molecular Foundations, Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Greg Collinge
- Basic & Applied Molecular Foundations, Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Loukas Kollias
- Basic & Applied Molecular Foundations, Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Manh-Thuong Nguyen
- Basic & Applied Molecular Foundations, Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Vassiliki-Alexandra Glezakou
- Basic & Applied Molecular Foundations, Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Roger Rousseau
- Basic & Applied Molecular Foundations, Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
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21
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Galimberti DR, Sauer J. Chemically Accurate Vibrational Free Energies of Adsorption from Density Functional Theory Molecular Dynamics: Alkanes in Zeolites. J Chem Theory Comput 2021; 17:5849-5862. [PMID: 34459582 PMCID: PMC8444336 DOI: 10.1021/acs.jctc.1c00519] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
We present a methodology
to compute, at reduced computational cost,
Gibbs free energies, enthalpies, and entropies of adsorption from
molecular dynamics. We calculate vibrational partition functions from
vibrational energies, which we obtain from the vibrational density
of states by projection on the normal modes. The use of a set of well-chosen
reference structures along the trajectories accounts for the anharmonicities
of the modes. For the adsorption of methane, ethane, and propane in
the H-CHA zeolite, we limit our treatment to a set of vibrational
modes localized at the adsorption site (zeolitic OH group) and the
alkane molecule interacting with it. Only two short trajectories (1–20
ps) are required to reach convergence (<1 kJ/mol) for the thermodynamic
functions. The mean absolute deviations from the experimentally measured
values are 2.6, 2.8, and 4.7 kJ/mol for the Gibbs free energy, the
enthalpy, and the entropy term (−TΔS),
respectively. In particular, the entropy terms show a major improvement
compared to the harmonic approximation and almost reach the accuracy
of the previous use of anharmonic frequencies obtained with curvilinear
distortions of individual modes. The thermodynamic functions so obtained
follow the trend of the experimental values for methane, ethane, and
propane, and the Gibbs free energy of adsorption at experimental conditions
is correctly predicted to change from positive for methane (5.9 kJ/mol)
to negative for ethane (−4.8 kJ/mol) and propane (−7.1
kJ/mol).
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Affiliation(s)
- Daria Ruth Galimberti
- Institut für Chemie, Humboldt-Universität, Unter den Linden 6, 10117 Berlin, Germany.,Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Joachim Sauer
- Institut für Chemie, Humboldt-Universität, Unter den Linden 6, 10117 Berlin, Germany
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22
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Ma S, Liu ZP. The Role of Zeolite Framework in Zeolite Stability and Catalysis from Recent Atomic Simulation. Top Catal 2021. [DOI: 10.1007/s11244-021-01473-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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23
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Pracht P, Grimme S. Calculation of absolute molecular entropies and heat capacities made simple. Chem Sci 2021; 12:6551-6568. [PMID: 34040731 PMCID: PMC8139639 DOI: 10.1039/d1sc00621e] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 03/24/2021] [Indexed: 12/25/2022] Open
Abstract
We propose a fully-automated composite scheme for the accurate and numerically stable calculation of molecular entropies by efficiently combining density-functional theory (DFT), semi-empirical methods (SQM), and force-field (FF) approximations. The scheme is systematically expandable and can be integrated seamlessly with continuum-solvation models. Anharmonic effects are included through the modified rigid-rotor-harmonic-oscillator (msRRHO) approximation and the Gibbs-Shannon formula for extensive conformer ensembles (CEs), which are generated by a metadynamics search algorithm and are extrapolated to completeness. For the first time, variations of the ro-vibrational entropy over the CE are consistently accounted-for through a Boltzmann-population average. Extensive tests of the protocol with the two standard DFT approaches B97-3c and B3LYP-D3 reveal an unprecedented accuracy with mean deviations <1 cal mol-1 K-1 (about <1-2%) for the total gas phase molecular entropy of medium-sized molecules. Even for the hardship case of extremely flexible linear alkanes (C14H30-C16H34), errors are only about 3 cal mol-1 K-1. Comprehensive tests indicate a relatively strong variation of the conformational entropy on the underlying level of theory for typical drug molecules, inferring the complex potential energy surfaces as the main source of error. Furthermore, we show some application examples for the calculation of free energy differences in typical chemical reactions.
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Affiliation(s)
- Philipp Pracht
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn Beringstr. 4 53115 Bonn Germany +49-228-73-2351
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn Beringstr. 4 53115 Bonn Germany +49-228-73-2351
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24
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25
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Amsler J, Plessow PN, Studt F, Bučko T. Anharmonic Correction to Adsorption Free Energy from DFT-Based MD Using Thermodynamic Integration. J Chem Theory Comput 2021; 17:1155-1169. [PMID: 33482059 DOI: 10.1021/acs.jctc.0c01022] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Adsorption processes are often governed by weak interactions for which the estimation of entropy contributions by means of the harmonic approximation is prone to be inaccurate. Thermodynamic integration (TI) from the harmonic to the fully interacting system (λ-path integration) can be used to compute anharmonic corrections. Here, we combine TI with (curvilinear) internal coordinates in periodic systems to make the formalism available in computational studies. Our implementation of ab initio molecular dynamics in VASP is independent of the reaction path and can be thus applied to study adsorption processes relative to the gas phase and does hence provide a useful tool for computational catalysis. We discuss the application of the approach on three model systems for which exact semianalytical solutions exist and illustrate and quantify the importance of anharmonic vibrations, hindered rotations, and hindered translations (dissociation). Eventually, we apply the method to study the adsorption of small adsorbates in a zeolite (H-SSZ-13).
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Affiliation(s)
- Jonas Amsler
- Institute of Catalysis Research and Technology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Philipp N Plessow
- Institute of Catalysis Research and Technology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Felix Studt
- Institute of Catalysis Research and Technology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.,Institute for Chemical Technology and Polymer Chemistry, Karlsruhe Institute of Technology, Kaiserstr. 12, 76131 Karlsruhe, Germany
| | - 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
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26
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Devi S, Tyagi A, Prasad V. Thermal behaviour of hindered rotor in static electric and laser field. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 240:118538. [PMID: 32526400 DOI: 10.1016/j.saa.2020.118538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 05/01/2020] [Accepted: 05/22/2020] [Indexed: 06/11/2023]
Abstract
We solve exactly the time independent Schrödinger equation (TISE) for hindered rotor confined in well shaped potential. Afterwards, the confined system is subjected to interact with laser and static electric field. TISE for the dressed confined rotor is solved using standard numerical method to get energy spectrum and eigenfunctions. Dependence of orientation and alignment parameters on static electric field and confining potential is studied. We also compute thermal properties like entropy and heat capacity of the system under consideration using canonical partition within statistical thermodynamic formalism. We have also studied the effect of external field parameters, confinement strength and temperature on these thermal properties.
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Affiliation(s)
- Sumana Devi
- Department of Physics and Astrophysics, University of Delhi, Delhi 110007, India; Department of Physics, Miranda House College, University of Delhi, Delhi 110007, India.
| | - Ashish Tyagi
- Department of Physics, Swami Shradhanand College, University of Delhi, Delhi 110036, India
| | - Vinod Prasad
- Department of Physics, Swami Shradhanand College, University of Delhi, Delhi 110036, India.
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27
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Clustering of alkanols confined in chabazite zeolites: Kinetic implications for dehydration of methanol-ethanol mixtures. J Catal 2020. [DOI: 10.1016/j.jcat.2020.07.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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28
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Guan E, Ciston J, Bare SR, Runnebaum RC, Katz A, Kulkarni A, Kronawitter CX, Gates BC. Supported Metal Pair-Site Catalysts. ACS Catal 2020. [DOI: 10.1021/acscatal.0c02000] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Erjia Guan
- Department of Chemical Engineering, University of California, Davis, California 95616, United States
| | - Jim Ciston
- National Center for Electron Microscopy Facility, Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Simon R. Bare
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Ron C. Runnebaum
- Department of Chemical Engineering, University of California, Davis, California 95616, United States
- Department of Viticulture & Enology, University of California, Davis, California 95616, United States
| | - Alexander Katz
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Ambarish Kulkarni
- Department of Chemical Engineering, University of California, Davis, California 95616, United States
| | - Coleman X. Kronawitter
- Department of Chemical Engineering, University of California, Davis, California 95616, United States
| | - Bruce C. Gates
- Department of Chemical Engineering, University of California, Davis, California 95616, United States
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29
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Collinge G, Yuk SF, Nguyen MT, Lee MS, Glezakou VA, Rousseau R. Effect of Collective Dynamics and Anharmonicity on Entropy in Heterogenous Catalysis: Building the Case for Advanced Molecular Simulations. ACS Catal 2020. [DOI: 10.1021/acscatal.0c01501] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Greg Collinge
- Basic & Applied Molecular Foundations, Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Simuck F. Yuk
- Basic & Applied Molecular Foundations, Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Manh-Thuong Nguyen
- Basic & Applied Molecular Foundations, Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Mal-Soon Lee
- Basic & Applied Molecular Foundations, Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Vassiliki-Alexandra Glezakou
- Basic & Applied Molecular Foundations, Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Roger Rousseau
- Basic & Applied Molecular Foundations, Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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30
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Yuk SF, Collinge G, Nguyen MT, Lee MS, Glezakou VA, Rousseau R. Selective acetylene hydrogenation over single metal atoms supported on Fe3O4(001): A first-principle study. J Chem Phys 2020; 152:154703. [DOI: 10.1063/1.5142748] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Simuck F. Yuk
- Basic & Applied Molecular Foundations, Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - Greg Collinge
- Basic & Applied Molecular Foundations, Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - Manh-Thuong Nguyen
- Basic & Applied Molecular Foundations, Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - Mal-Soon Lee
- Basic & Applied Molecular Foundations, Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - Vassiliki-Alexandra Glezakou
- Basic & Applied Molecular Foundations, Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - Roger Rousseau
- Basic & Applied Molecular Foundations, Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
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31
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Rzepa C, Siderius DW, Hatch HW, Shen VK, Rangarajan S, Mittal J. Computational Investigation of Correlations in Adsorbate Entropy for Pure-Silica Zeolite Adsorbents. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2020; 124:10.1021/acs.jpcc.0c02671. [PMID: 33643514 PMCID: PMC7905991 DOI: 10.1021/acs.jpcc.0c02671] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Vast numbers of unstudied hypothetical porous frameworks continue to spark interest in optimizing adsorption and catalytic processes. Evaluating the use of such materials depends on the accessibility of thermodynamic metrics such as the free energy, which, in turn, depend on the satisfactory estimation or calculation of the adsorption entropy, which often remains elusive. Previous works using simulations and experimental data have demonstrated relationships between the entropy and system descriptors, allowing for sensible predictions based on more-easily obtained physical parameters. However, the resultant conclusions were either based on experimental data for industrially relevant alkanes or lacked a significant sample size. In this paper, we evaluate correlations between gas-phase and adsorbed-phase entropies for a larger and more chemically diverse set of adsorbate molecules by using force fields and statistical mechanical expressions to calculate those entropies. In total, we perform calculations for 37 molecules across 10 chemical categories available in the TraPPE force field set, as adsorbed in five siliceous zeolites. Our results show that linear correlations between the gas- and adsorbed-phase entropies persist for the larger and diverse set of adsorbate molecules studied here, proving a broader applicability and justifying the use of simple correlations for many adsorbates and, presumably, adsorbent materials.
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Affiliation(s)
- Christopher Rzepa
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, PA 18015, USA
| | - Daniel W. Siderius
- Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, MD 20899-8320, USA
| | - Harold W. Hatch
- Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, MD 20899-8320, USA
| | - Vincent K. Shen
- Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, MD 20899-8320, USA
| | - Srinivas Rangarajan
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, PA 18015, USA
| | - Jeetain Mittal
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, PA 18015, USA
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Kundu A, Sillar K, Sauer J. Predicting adsorption selectivities from pure gas isotherms for gas mixtures in metal-organic frameworks. Chem Sci 2019; 11:643-655. [PMID: 34123036 PMCID: PMC8146500 DOI: 10.1039/c9sc03008e] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We perform Grand Canonical Monte Carlo simulations on a lattice of Mg2+ sites (GCMC) for adsorption of four binary A/B mixtures, CH4/N2, CO/N2, CO2/N2, and CO2/CH4, in the metal–organic framework Mg2(2,5-dioxidobenzedicarboxylate), also known as CPO-27–Mg or Mg–MOF-74. We present a mean field co-adsorption isotherm model and show that its predictions agree with the GCMC results if the same quantum chemical ab initio data are used for Gibbs free energies of adsorption at the individual sites and for lateral interaction energies between the same, A⋯A and B⋯B, and unlike, A⋯B, adsorbed molecules. We use both approaches to test the assumption underlying Ideal Adsorbed Solution Theory (IAST), namely approximating A⋯B interaction energies as the arithmetic mean of A⋯A and B⋯B interaction energies. While IAST works well for mixtures with weak lateral interactions, CH4/N2 and CO/N2, the deviations are large for mixtures with stronger lateral interactions, CO2/N2 and CO2/CH4. Motivated by the theory of London dispersion forces, we propose use of the geometric mean instead of the arithmetic mean and achieve substantial improvements. For CO2/CH4, the lateral interactions become anisotropic. To include this in the geometric mean co-adsorption model, we introduce an anisotropy factor. We propose a protocol, named co-adsorption mean field theory (CAMT), for co-adsorption selectivity prediction from known (experiment or simulation) pure component isotherms which is similar to the IAST protocol but uses the geometric mean to approximate mixed pair interaction energies and yields improved results for non-ideal mixtures. A new mixing rule (geometric mean) is proposed with substantial improvements compared to the widely used ideal adsorbed solution theory for adsorbates with strong lateral interactions.![]()
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Affiliation(s)
- Arpan Kundu
- Humboldt Universität zu Berlin, Institut für Chemie Unter den Linden 6 10099 Berlin Germany
| | - Kaido Sillar
- Humboldt Universität zu Berlin, Institut für Chemie Unter den Linden 6 10099 Berlin Germany .,University of Tartu, Institute of Chemistry Ravila 14a 50411 Tartu Estonia
| | - Joachim Sauer
- Humboldt Universität zu Berlin, Institut für Chemie Unter den Linden 6 10099 Berlin Germany
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Tian H, Rzepa C, Upadhyay R, Rangarajan S. Estimating vibrational and thermodynamic properties of adsorbates with uncertainty using data driven surrogates. AIChE J 2019. [DOI: 10.1002/aic.16838] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Huijie Tian
- Department of Chemical & Biomolecular Engineering Lehigh University Bethlehem Pennsylvania
| | - Christopher Rzepa
- Department of Chemical & Biomolecular Engineering Lehigh University Bethlehem Pennsylvania
| | - Ronak Upadhyay
- Department of Chemical & Biomolecular Engineering Lehigh University Bethlehem Pennsylvania
| | - Srinivas Rangarajan
- Department of Chemical & Biomolecular Engineering Lehigh University Bethlehem Pennsylvania
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Belviso F, Claerbout VEP, Comas-Vives A, Dalal NS, Fan FR, Filippetti A, Fiorentini V, Foppa L, Franchini C, Geisler B, Ghiringhelli LM, Groß A, Hu S, Íñiguez J, Kauwe SK, Musfeldt JL, Nicolini P, Pentcheva R, Polcar T, Ren W, Ricci F, Ricci F, Sen HS, Skelton JM, Sparks TD, Stroppa A, Urru A, Vandichel M, Vavassori P, Wu H, Yang K, Zhao HJ, Puggioni D, Cortese R, Cammarata A. Viewpoint: Atomic-Scale Design Protocols toward Energy, Electronic, Catalysis, and Sensing Applications. Inorg Chem 2019; 58:14939-14980. [DOI: 10.1021/acs.inorgchem.9b01785] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Florian Belviso
- Department of Control Engineering, Czech Technical University in Prague, Technicka 2, 16627 Prague 6, Czech Republic
| | - Victor E. P. Claerbout
- Department of Control Engineering, Czech Technical University in Prague, Technicka 2, 16627 Prague 6, Czech Republic
| | - Aleix Comas-Vives
- Department of Chemistry, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Catalonia, Spain
| | - Naresh S. Dalal
- National High Magnet Field Lab, Tallahassee, Florida 32310, United States
- Department of Chemistry & Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
| | - Feng-Ren Fan
- Laboratory for Computational Physical Sciences (MOE), State Key Laboratory of Surface Physics, and Department of Physics, Fudan University, Shanghai 200433, China
| | - Alessio Filippetti
- Department of Physics at University of Cagliari, and CNR-IOM, UOS Cagliari, Cittadella Universitaria, I-09042 Monserrato (CA), Italy
| | - Vincenzo Fiorentini
- Department of Physics at University of Cagliari, and CNR-IOM, UOS Cagliari, Cittadella Universitaria, I-09042 Monserrato (CA), Italy
| | - Lucas Foppa
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1-5, CH-8093 Zürich, Switzerland
| | - Cesare Franchini
- Faculty of Physics and Center for Computational Materials Science, University of Vienna, Sensengasse 8, A-1090 Vienna, Austria
- Dipartimento di Fisica e Astronomia, Università di Bologna, Bologna 40127, Italy
| | - Benjamin Geisler
- Department of Physics and Center for Nanointegration (CENIDE), Universität Duisburg-Essen, Lotharstr. 1, Duisburg 47057, Germany
| | | | - Axel Groß
- Electrochemical Energy Storage, Helmholtz Institut Ulm, Ulm 89069, Germany
- Institute of Theoretical Chemistry, Ulm University, Ulm 89069, Germany
| | - Shunbo Hu
- Department of Physics, Materials Genome Institute, and International Center of Quantum and Molecular Structures, Shanghai University, 99 Shangda Road, Shanghai 200444, China
| | - Jorge Íñiguez
- Materials Research and Technology Department, Luxembourg Institute of Science and Technology, Avenue des Hauts-Fourneaux 5, L-4362 Esch/Alzette, Luxembourg
- Physics and Materials Research Unit, University of Luxembourg, Rue du Brill 41, Belvaux L-4422, Luxembourg
| | - Steven Kaai Kauwe
- Materials Science & Engineering Department, University of Utah, 122 Central Campus Drive, Salt Lake City, Utah 84112, United States
| | - Janice L. Musfeldt
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Paolo Nicolini
- Department of Control Engineering, Czech Technical University in Prague, Technicka 2, 16627 Prague 6, Czech Republic
| | - Rossitza Pentcheva
- Department of Physics and Center for Nanointegration (CENIDE), Universität Duisburg-Essen, Lotharstr. 1, Duisburg 47057, Germany
| | - Tomas Polcar
- Department of Control Engineering, Czech Technical University in Prague, Technicka 2, 16627 Prague 6, Czech Republic
| | - Wei Ren
- Department of Physics, Materials Genome Institute, and International Center of Quantum and Molecular Structures, Shanghai University, 99 Shangda Road, Shanghai 200444, China
| | - Fabio Ricci
- Physique Theorique des Materiaux, Universite de Liege, Sart-Tilman B-4000, Belgium
| | - Francesco Ricci
- Institute of Condensed Matter and Nanosciences, Universite Catholique de Louvain, Chemin des Etoiles 8, Louvain-la-Neuve B-1348, Belgium
| | - Huseyin Sener Sen
- Department of Control Engineering, Czech Technical University in Prague, Technicka 2, 16627 Prague 6, Czech Republic
| | - Jonathan Michael Skelton
- Department of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Taylor D. Sparks
- Materials Science & Engineering Department, University of Utah, 122 Central Campus Drive, Salt Lake City, Utah 84112, United States
| | - Alessandro Stroppa
- CNR-SPIN, Department of Physical Sciences and Chemistry, Universita degli Studi dell’Aquila, Via Vetoio, Coppito (AQ) 67010, Italy
| | - Andrea Urru
- Department of Physics at University of Cagliari, and CNR-IOM, UOS Cagliari, Cittadella Universitaria, I-09042 Monserrato (CA), Italy
| | - Matthias Vandichel
- Department of Chemical Sciences and Bernal Institute, Limerick University, Limerick, Ireland
- Department of Chemistry and Material Science and Department of Applied Physics, Aalto University, Espoo 02150, Finland
| | - Paolo Vavassori
- CIC nanoGUNE, San Sebastian E-20018, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao 48013, Spain
| | - Hua Wu
- Laboratory for Computational Physical Sciences (MOE), State Key Laboratory of Surface Physics, and Department of Physics, Fudan University, Shanghai 200433, China
- Collaborative Innovation Center of Advanced Microstructures, Nanjing 210093, China
| | - Ke Yang
- Laboratory for Computational Physical Sciences (MOE), State Key Laboratory of Surface Physics, and Department of Physics, Fudan University, Shanghai 200433, China
| | - Hong Jian Zhao
- Materials Research and Technology Department, Luxembourg Institute of Science and Technology, Avenue des Hauts-Fourneaux 5, L-4362 Esch/Alzette, Luxembourg
- Physics Department and Institute for Engineering, University of Arkansas, Fayetteville, Arkansas 72701,United States
| | - Danilo Puggioni
- Department of Materials Science and Engineering, Northwestern University, 2220 Campus Drive, Evanston, Illinois 60208, United States
| | - Remedios Cortese
- Department of Physics and Chemistry, Università degli Studi di Palermo, Viale delle Scienze ed. 17, Palermo 90128, Italy
| | - Antonio Cammarata
- Department of Control Engineering, Czech Technical University in Prague, Technicka 2, 16627 Prague 6, Czech Republic
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35
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Bruix A, Margraf JT, Andersen M, Reuter K. First-principles-based multiscale modelling of heterogeneous catalysis. Nat Catal 2019. [DOI: 10.1038/s41929-019-0298-3] [Citation(s) in RCA: 131] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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36
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Harvey JN, Himo F, Maseras F, Perrin L. Scope and Challenge of Computational Methods for Studying Mechanism and Reactivity in Homogeneous Catalysis. ACS Catal 2019. [DOI: 10.1021/acscatal.9b01537] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Jeremy N. Harvey
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
| | - Fahmi Himo
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Feliu Maseras
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Avgda. Països Catalans, 16, 43007 Tarragona, Catalonia, Spain
| | - Lionel Perrin
- Univ Lyon, Université Claude Bernard Lyon 1, CPE Lyon, INSA Lyon, ICBMS, CNRS UMR 5246, 43 Bd. du 11 Novembre 1918, 69622 Villeurbanne, France
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37
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Matera S, Schneider WF, Heyden A, Savara A. Progress in Accurate Chemical Kinetic Modeling, Simulations, and Parameter Estimation for Heterogeneous Catalysis. ACS Catal 2019. [DOI: 10.1021/acscatal.9b01234] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sebastian Matera
- Fachbereich Mathematik and Informatik, Freie Universität, 14195 Berlin, Germany
| | - William F. Schneider
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Andreas Heyden
- Department of Chemical Engineering, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Aditya Savara
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
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38
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Bates JS, Bukowski BC, Harris JW, Greeley J, Gounder R. Distinct Catalytic Reactivity of Sn Substituted in Framework Locations and at Defect Grain Boundaries in Sn-Zeolites. ACS Catal 2019. [DOI: 10.1021/acscatal.9b01123] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Jason S. Bates
- Charles D. Davidson School of Chemical Engineering, Purdue University, 480 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Brandon C. Bukowski
- Charles D. Davidson School of Chemical Engineering, Purdue University, 480 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - James W. Harris
- Charles D. Davidson School of Chemical Engineering, Purdue University, 480 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Jeffrey Greeley
- Charles D. Davidson School of Chemical Engineering, Purdue University, 480 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Rajamani Gounder
- Charles D. Davidson School of Chemical Engineering, Purdue University, 480 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
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39
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Rybicki M, Sauer J. Ab Initio Prediction of Proton Exchange Barriers for Alkanes at Brønsted Sites of Zeolite H-MFI. J Am Chem Soc 2018; 140:18151-18161. [DOI: 10.1021/jacs.8b11228] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Marcin Rybicki
- Institut für Chemie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany
| | - Joachim Sauer
- Institut für Chemie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany
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40
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Grajciar L, Heard CJ, Bondarenko AA, Polynski MV, Meeprasert J, Pidko EA, Nachtigall P. Towards operando computational modeling in heterogeneous catalysis. Chem Soc Rev 2018; 47:8307-8348. [PMID: 30204184 PMCID: PMC6240816 DOI: 10.1039/c8cs00398j] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Indexed: 12/19/2022]
Abstract
An increased synergy between experimental and theoretical investigations in heterogeneous catalysis has become apparent during the last decade. Experimental work has extended from ultra-high vacuum and low temperature towards operando conditions. These developments have motivated the computational community to move from standard descriptive computational models, based on inspection of the potential energy surface at 0 K and low reactant concentrations (0 K/UHV model), to more realistic conditions. The transition from 0 K/UHV to operando models has been backed by significant developments in computer hardware and software over the past few decades. New methodological developments, designed to overcome part of the gap between 0 K/UHV and operando conditions, include (i) global optimization techniques, (ii) ab initio constrained thermodynamics, (iii) biased molecular dynamics, (iv) microkinetic models of reaction networks and (v) machine learning approaches. The importance of the transition is highlighted by discussing how the molecular level picture of catalytic sites and the associated reaction mechanisms changes when the chemical environment, pressure and temperature effects are correctly accounted for in molecular simulations. It is the purpose of this review to discuss each method on an equal footing, and to draw connections between methods, particularly where they may be applied in combination.
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Affiliation(s)
- Lukáš Grajciar
- Department of Physical and Macromolecular Chemistry
, Faculty of Science
, Charles University in Prague
,
128 43 Prague 2
, Czech Republic
.
;
;
| | - Christopher J. Heard
- Department of Physical and Macromolecular Chemistry
, Faculty of Science
, Charles University in Prague
,
128 43 Prague 2
, Czech Republic
.
;
;
| | - Anton A. Bondarenko
- TheoMAT group
, ITMO University
,
Lomonosova 9
, St. Petersburg
, 191002
, Russia
| | - Mikhail V. Polynski
- TheoMAT group
, ITMO University
,
Lomonosova 9
, St. Petersburg
, 191002
, Russia
| | - Jittima Meeprasert
- Inorganic Systems Engineering group
, Department of Chemical Engineering
, Faculty of Applied Sciences
, Delft University of Technology
,
Van der Maasweg 9
, 2629 HZ Delft
, The Netherlands
.
| | - Evgeny A. Pidko
- TheoMAT group
, ITMO University
,
Lomonosova 9
, St. Petersburg
, 191002
, Russia
- Inorganic Systems Engineering group
, Department of Chemical Engineering
, Faculty of Applied Sciences
, Delft University of Technology
,
Van der Maasweg 9
, 2629 HZ Delft
, The Netherlands
.
| | - Petr Nachtigall
- Department of Physical and Macromolecular Chemistry
, Faculty of Science
, Charles University in Prague
,
128 43 Prague 2
, Czech Republic
.
;
;
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41
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Vummaleti SVC, Genest A, Kuriakose N, Rösch N. Ethene Dimerization and Hydrogenation over a Zeolite-Supported Rh(I)-Carbonyl Complex: Mechanistic Insights from DFT Modeling. ACS Catal 2018. [DOI: 10.1021/acscatal.8b02573] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sai V. C. Vummaleti
- Institute of High Performance Computing, Agency for Science, Technology and Research, 1 Fusionopolis Way, #16-16 Connexis, Singapore 138632, Singapore
| | - Alexander Genest
- Institute of High Performance Computing, Agency for Science, Technology and Research, 1 Fusionopolis Way, #16-16 Connexis, Singapore 138632, Singapore
| | - Nishamol Kuriakose
- Institute of High Performance Computing, Agency for Science, Technology and Research, 1 Fusionopolis Way, #16-16 Connexis, Singapore 138632, Singapore
| | - Notker Rösch
- Institute of High Performance Computing, Agency for Science, Technology and Research, 1 Fusionopolis Way, #16-16 Connexis, Singapore 138632, Singapore
- Department Chemie and Catalysis Research Center, Technische Universität München, 85747 Garching, Germany
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42
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Bukowski BC, Bates JS, Gounder R, Greeley J. First principles, microkinetic, and experimental analysis of Lewis acid site speciation during ethanol dehydration on Sn-Beta zeolites. J Catal 2018. [DOI: 10.1016/j.jcat.2018.07.012] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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43
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De Wispelaere K, Martínez-Espín JS, Hoffmann MJ, Svelle S, Olsbye U, Bligaard T. Understanding zeolite-catalyzed benzene methylation reactions by methanol and dimethyl ether at operating conditions from first principle microkinetic modeling and experiments. Catal Today 2018. [DOI: 10.1016/j.cattod.2018.02.042] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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44
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Proppe J, Husch T, Simm GN, Reiher M. Uncertainty quantification for quantum chemical models of complex reaction networks. Faraday Discuss 2018; 195:497-520. [PMID: 27730243 DOI: 10.1039/c6fd00144k] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
For the quantitative understanding of complex chemical reaction mechanisms, it is, in general, necessary to accurately determine the corresponding free energy surface and to solve the resulting continuous-time reaction rate equations for a continuous state space. For a general (complex) reaction network, it is computationally hard to fulfill these two requirements. However, it is possible to approximately address these challenges in a physically consistent way. On the one hand, it may be sufficient to consider approximate free energies if a reliable uncertainty measure can be provided. On the other hand, a highly resolved time evolution may not be necessary to still determine quantitative fluxes in a reaction network if one is interested in specific time scales. In this paper, we present discrete-time kinetic simulations in discrete state space taking free energy uncertainties into account. The method builds upon thermo-chemical data obtained from electronic structure calculations in a condensed-phase model. Our kinetic approach supports the analysis of general reaction networks spanning multiple time scales, which is here demonstrated for the example of the formose reaction. An important application of our approach is the detection of regions in a reaction network which require further investigation, given the uncertainties introduced by both approximate electronic structure methods and kinetic models. Such cases can then be studied in greater detail with more sophisticated first-principles calculations and kinetic simulations.
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Affiliation(s)
- Jonny Proppe
- Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland.
| | - Tamara Husch
- Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland.
| | - Gregor N Simm
- Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland.
| | - Markus Reiher
- Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland.
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45
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Zhao P, Ye L, Sun Z, Lo BTW, Woodcock H, Huang C, Tang C, Kirkland AI, Mei D, Edman Tsang SC. Entrapped Single Tungstate Site in Zeolite for Cooperative Catalysis of Olefin Metathesis with Brønsted Acid Site. J Am Chem Soc 2018; 140:6661-6667. [PMID: 29660275 DOI: 10.1021/jacs.8b03012] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Industrial olefin metathesis catalysts generally suffer from low reaction rates and require harsh reaction conditions for moderate activities. This is due to their inability to prevent metathesis active sites (MASs) from aggregation and their intrinsic poor adsorption and activation of olefin molecules. Here, isolated tungstate species as single molecular MASs are immobilized inside zeolite pores by Brønsted acid sites (BASs) on the inner surface. It is demonstrated that unoccupied BASs in atomic proximity to MASs enhance olefin adsorption and facilitate the formation of metallocycle intermediates in a stereospecific manner. Thus, effective cooperative catalysis takes place over the BAS-MAS pair inside the zeolite cavity. In consequence, for the cross-metathesis of ethene and trans-2-butene to propene, under mild reaction conditions, the propene production rate over WO x/USY is ca. 7300 times that over the industrial WO3/SiO2-based catalyst. A propene yield up to 79% (80% selectivity) without observable deactivation was obtained over WO x/USY for a wide range of reaction conditions.
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Affiliation(s)
- Pu Zhao
- Wolfson Catalysis Centre, Department of Chemistry , University of Oxford , Oxford OX1 3QR , U.K
| | - Lin Ye
- Wolfson Catalysis Centre, Department of Chemistry , University of Oxford , Oxford OX1 3QR , U.K
| | - Zhenyu Sun
- Wolfson Catalysis Centre, Department of Chemistry , University of Oxford , Oxford OX1 3QR , U.K
| | - Benedict T W Lo
- Wolfson Catalysis Centre, Department of Chemistry , University of Oxford , Oxford OX1 3QR , U.K
| | - Harry Woodcock
- Wolfson Catalysis Centre, Department of Chemistry , University of Oxford , Oxford OX1 3QR , U.K
| | - Chen Huang
- Department of Materials , University of Oxford , Oxford OX1 3PH , U.K
| | - Chiu Tang
- Diamond Light Source Ltd. , Harwell Science and Innovation Campus , Didcot OX11 0DE , U.K
| | - Angus I Kirkland
- Department of Materials , University of Oxford , Oxford OX1 3PH , U.K.,Diamond Light Source Ltd. , Harwell Science and Innovation Campus , Didcot OX11 0DE , U.K
| | - Donghai Mei
- Physical and Computational Sciences Directorate & Institute for Integrated Catalysis , Pacific Northwest National Laboratory , PO Box 999 , Richland , Washington 99354 , United States
| | - Shik Chi Edman Tsang
- Wolfson Catalysis Centre, Department of Chemistry , University of Oxford , Oxford OX1 3QR , U.K
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46
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Van der Mynsbrugge J, Janda A, Lin LC, Van Speybroeck V, Head-Gordon M, Bell AT. Understanding Brønsted-Acid Catalyzed Monomolecular Reactions of Alkanes in Zeolite Pores by Combining Insights from Experiment and Theory. Chemphyschem 2018; 19:341-358. [PMID: 29239509 DOI: 10.1002/cphc.201701084] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 12/08/2017] [Indexed: 11/11/2022]
Abstract
Acidic zeolites are effective catalysts for the cracking of large hydrocarbon molecules into lower molecular weight products required for transportation fuels. However, the ways in which the zeolite structure affects the catalytic activity at Brønsted protons are not fully understood. One way to characterize the influence of the zeolite structure on the catalysis is to study alkane cracking and dehydrogenation at very low conversion, conditions for which the kinetics are well defined. To understand the effects of zeolite structure on the measured rate coefficient (kapp ), it is necessary to identify the equilibrium constant for adsorption into the reactant state (Kads-H+ ) and the intrinsic rate coefficient of the reaction (kint ) at reaction temperatures, since kapp is proportional to the product of Kads-H+ and kint . We show that Kads-H+ cannot be calculated from experimental adsorption data collected near ambient temperature, but can, however, be estimated accurately from configurational-bias Monte Carlo (CBMC) simulations. Using monomolecular cracking and dehydrogenation of C3 -C6 alkanes as an example, we review recent efforts aimed at elucidating the influence of the acid site location and the zeolite framework structure on the observed values of kapp and its components, Kads-H+ and kint .
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Affiliation(s)
- Jeroen Van der Mynsbrugge
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA.,Center for Molecular Modeling, Ghent University, Tech Lane Ghent Science Park Campus A, Technologiepark 903, 9052, Zwijnaarde, Belgium
| | - Amber Janda
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA.,Present address: Department of Chemical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Li-Chiang Lin
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, 151 W. Woodruff Ave., Columbus, OH, 43210, USA
| | - Veronique Van Speybroeck
- Center for Molecular Modeling, Ghent University, Tech Lane Ghent Science Park Campus A, Technologiepark 903, 9052, Zwijnaarde, Belgium
| | - 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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47
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Besora M, Vidossich P, Lledós A, Ujaque G, Maseras F. Calculation of Reaction Free Energies in Solution: A Comparison of Current Approaches. J Phys Chem A 2018; 122:1392-1399. [DOI: 10.1021/acs.jpca.7b11580] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Maria Besora
- Institute
of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Avinguda Països Catalans 16, 43007 Tarragona, Catalonia, Spain
| | - Pietro Vidossich
- Departament
de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola
del Valles, Catalonia, Spain
- COBO
Computational Bio-Organic Chemistry Bogotá, Department of Chemistry, Universidad de los Andes, Carrera 1 No. 18A 10, 111711 Bogotá, Colombia
| | - Agustí Lledós
- Departament
de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola
del Valles, Catalonia, Spain
| | - Gregori Ujaque
- Departament
de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola
del Valles, Catalonia, Spain
| | - Feliu Maseras
- Institute
of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Avinguda Països Catalans 16, 43007 Tarragona, Catalonia, Spain
- Departament
de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola
del Valles, Catalonia, Spain
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48
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Li H, Paolucci C, Schneider WF. Zeolite Adsorption Free Energies from ab Initio Potentials of Mean Force. J Chem Theory Comput 2018; 14:929-938. [PMID: 29232513 DOI: 10.1021/acs.jctc.7b00716] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The ability of metal-exchanged zeolites to chemisorb small gas molecules is key to their performance as heterogeneous catalysts and gas-separating agents. Here, we propose and evaluate an ab initio potential of mean force (PMF) method for computing adsorption free energies of representative small molecules to Cu-exchanged sites in SSZ-13 zeolite. We show that Cu ions are mobilized by adsorbates and, as a result, computed free energies are significantly more negative than those obtained from a conventional harmonic oscillator model. PMF-derived free energies are consistent with available experiment and, in many cases, with a dynamics-based quasi-harmonic analysis (QHA). The PMF approach avoids the artificial partitioning of degrees of freedom intrinsic to the QHA. On the basis of the PMF results, we propose a simple correlation to estimate free energies from computed adsorption energies and gas-phase entropies.
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Affiliation(s)
- Hui Li
- Department of Chemical and Biomolecular Engineering, University of Notre Dame , 182 Fitzpatrick Hall, Notre Dame, Indiana 46556, United States
| | - Christopher Paolucci
- Department of Chemical and Biomolecular Engineering, University of Notre Dame , 182 Fitzpatrick Hall, Notre Dame, Indiana 46556, United States
| | - William F Schneider
- Department of Chemical and Biomolecular Engineering, University of Notre Dame , 182 Fitzpatrick Hall, Notre Dame, Indiana 46556, United States
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Piccini G, Alessio M, Sauer J. Ab initio study of methanol and ethanol adsorption on Brønsted sites in zeolite H-MFI. Phys Chem Chem Phys 2018; 20:19964-19970. [DOI: 10.1039/c8cp03632b] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ethanol in zeolite H-MFI: passing from DFT to MP2 and taking anharmonicity into account changes enthalpies of adsorption significantly.
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Affiliation(s)
- GiovanniMaria Piccini
- Institut für Chemie
- Humboldt Universität zu Berlin
- 10099 Berlin
- Germany
- Department of Chemistry and Applied Biosciences
| | | | - Joachim Sauer
- Institut für Chemie
- Humboldt Universität zu Berlin
- 10099 Berlin
- Germany
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50
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Li S, Zheng Y, Gao F, Szanyi J, Schneider WF. Experimental and Computational Interrogation of Fast SCR Mechanism and Active Sites on H-Form SSZ-13. ACS Catal 2017. [DOI: 10.1021/acscatal.7b01319] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sichi Li
- Department
of Chemical and Biomolecular Engineering, University of Notre Dame, Notre
Dame, Indiana 46556, United States
| | - Yang Zheng
- Institute
for Integrated Catalysis, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
| | - Feng Gao
- Institute
for Integrated Catalysis, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
| | - Janos Szanyi
- Institute
for Integrated Catalysis, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
| | - William F. Schneider
- Department
of Chemical and Biomolecular Engineering, University of Notre Dame, Notre
Dame, Indiana 46556, United States
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