CatMAP: A Software Package for Descriptor-Based Microkinetic Mapping of Catalytic Trends
TL;DR: The “CatMAP” Python module seeks to standardize and automate many of the mathematical routines necessary to move from “descriptor space” to reaction rates for heterogeneous (electro) catalysts and presents the underlying algorithms and mathematical expressions both generally and via an example for the CO oxidation reaction.
Abstract: Descriptor-based analysis is a powerful tool for understanding the trends across various catalysts. In general, the rate of a reaction over a given catalyst is a function of many parameters—reaction energies, activation barriers, thermodynamic conditions, etc. The high dimensionality of this problem makes it very difficult and expensive to solve completely, and even a full solution would not give much insight into the rational design of new catalysts. The descriptor-based approach seeks to determine a few “descriptors” upon which the other parameters are dependent. By doing this it is possible to reduce the dimensionality of the problem—preferably to 1 or 2 descriptors—thus greatly reducing computational efforts and simultaneously increasing the understanding of trends in catalysis. The “CatMAP” Python module seeks to standardize and automate many of the mathematical routines necessary to move from “descriptor space” to reaction rates for heterogeneous (electro) catalysts. The module is designed to be both flexible and powerful, and is available for free online. A “reaction model” can be fully defined by a configuration file, thus no new programming is necessary to change the complexity or assumptions of a model. Furthermore, various steps in the process of moving from descriptors to reaction rates have been abstracted into separate Python classes, making it easy to change the methods used or add new functionality. This work discusses the structure of the code and presents the underlying algorithms and mathematical expressions both generally and via an example for the CO oxidation reaction.
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TL;DR: An understanding of trends in electrocatalytic activity for carbon dioxide reduction over different metal catalysts is presented that rationalize a number of experimental observations including the selectivity with respect to the competing hydrogen evolution reaction.
Abstract: Electrochemical carbon dioxide reduction to fuels presents one of the great challenges in chemistry Herein we present an understanding of trends in electrocatalytic activity for carbon dioxide reduction over different metal catalysts that rationalize a number of experimental observations including the selectivity with respect to the competing hydrogen evolution reaction We also identify two design criteria for more active catalysts The understanding is based on density functional theory calculations of activation energies for electrochemical carbon monoxide reduction as a basis for an electrochemical kinetic model of the process We develop scaling relations relating transition state energies to the carbon monoxide adsorption energy and determine the optimal value of this descriptor to be very close to that of copper
493 citations
TL;DR: The whole catalytic mechanism for conversion of N2 to NH3 on Fe3/θ-Al2O3(010) surface is studied, and an associative mechanism dominates over the dissociative mechanism, which is attributed to the large spin polarization, low oxidation state of iron, and multi-step redox capability of Fe3 cluster.
Abstract: The current industrial ammonia synthesis relies on Haber-Bosch process that is initiated by the dissociative mechanism, in which the adsorbed N2 dissociates directly, and thus is limited by Bronsted-Evans-Polanyi (BEP) relation. Here we propose a new strategy that an anchored Fe3 cluster on the θ-Al2O3(010) surface as a heterogeneous catalyst for ammonia synthesis from first-principles theoretical study and microkinetic analysis. We have studied the whole catalytic mechanism for conversion of N2 to NH3 on Fe3/θ-Al2O3(010), and find that an associative mechanism, in which the adsorbed N2 is first hydrogenated to NNH, dominates over the dissociative mechanism, which we attribute to the large spin polarization, low oxidation state of iron, and multi-step redox capability of Fe3 cluster. The associative mechanism liberates the turnover frequency (TOF) for ammonia production from the limitation due to the BEP relation, and the calculated TOF on Fe3/θ-Al2O3(010) is comparable to Ru B5 site.
374 citations
TL;DR: A microkinetic model for CO2 and CO reduction on copper is presented, based on ab initio simulations, to elucidate pH’s impact on competitive reaction pathways and elucidate how reaction conditions can lead to significant enhancements in selectivity and activity towards higher value C2 products.
Abstract: We present a microkinetic model for CO(2) reduction (CO(2)R) on Cu(211) towards C2 products, based on energetics estimated from an explicit solvent model. We show that the differences in both Tafel slopes and pH dependence for C1 vs C2 activity arise from differences in their multi-step mechanisms. We find the depletion in C2 products observed at high overpotential and high pH to arise from the 2nd order dependence of C-C coupling on CO coverage, which decreases due to competition from the C1 pathway. We further demonstrate that CO(2) reduction at a fixed pH yield similar activities, due to the facile kinetics for CO2 reduction to CO on Cu, which suggests C2 products to be favored for CO2R under alkaline conditions. The mechanistic insights of this work elucidate how reaction conditions can lead to significant enhancements in selectivity and activity towards higher value C2 products.
316 citations
TL;DR: The degree of rate control (DRC) is a mathematical approach for analyzing multistep reaction mechanisms that has proven very useful in catalysis research as discussed by the authors, which identifies the rate-controlling transition states and intermediates (i.e., those whose DRCs are large in magnitude).
Abstract: The “degree of rate control” (DRC) is a mathematical approach for analyzing multistep reaction mechanisms that has proven very useful in catalysis research. It identifies the “rate-controlling transition states and intermediates” (i.e., those whose DRCs are large in magnitude). Even in mechanisms with over 30 intermediates and transition states, these are generally just a few distinct chemical species whose energies, if they could be independently changed, would achieve a faster net reaction rate to the product of interest. For example, when there is a single “rate-determining step”, the DRC for its transition state (TS) is 1, which means (by definition) that if this TS’s energy could be decreased by kBT (where kB is Boltzmann’s constant and T is temperature), the net rate would increase by a factor of e. Because the (relative) energies of these key adsorbed intermediates and transition states can be adjusted by modifying the catalyst or solvent, or even a reactant’s molecular structure, the DRC values pr...
266 citations
22 Mar 2021
TL;DR: In this article, the authors reported that CO2 can dissociate at sulfur vacancies in MoS2 nanosheets to yield surface-bound CO and O at room temperature, thus enabling a highly efficient low-temperature hydrogenation of CO2 to methanol.
Abstract: The low-temperature hydrogenation of CO2 to methanol is of great significance for the recycling of this greenhouse gas to valuable products, however, it remains a great challenge due to the trade-off between catalytic activity and selectivity. Here, we report that CO2 can dissociate at sulfur vacancies in MoS2 nanosheets to yield surface-bound CO and O at room temperature, thus enabling a highly efficient low-temperature hydrogenation of CO2 to methanol. Multiple in situ spectroscopic and microscopic characterizations combined with theoretical calculations demonstrated that in-plane sulfur vacancies drive the selective hydrogenation of CO2 to methanol by inhibiting deep hydrogenolysis to methane, whereas edge vacancies facilitate excessive hydrogenation to methane. At 180 °C, the catalyst achieved a 94.3% methanol selectivity at a CO2 conversion of 12.5% over the in-plane sulfur vacancy-rich MoS2 nanosheets, which notably surpasses those of previously reported catalysts. This catalyst exhibited high stability for over 3,000 hours without any deactivation, rendering it a promising candidate for industrial application. The catalytic hydrogenation of CO2 to methanol is a crucial reaction for the recycling of this greenhouse gas, although the selection and related performance of commercial catalysts is still limited. Now, the authors introduce sulfur vacancy-rich MoS2 nanosheets as a superior catalyst for this process, rivalling the commercial benchmark system.
201 citations
References
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TL;DR: In this paper, the stability of reaction intermediates of electrochemical processes on the basis of electronic structure calculations was analyzed and a detailed description of the free energy landscape of the electrochemical oxygen reduction reaction over Pt(111) as a function of applied bias was presented.
Abstract: We present a method for calculating the stability of reaction intermediates of electrochemical processes on the basis of electronic structure calculations. We used that method in combination with detailed density functional calculations to develop a detailed description of the free-energy landscape of the electrochemical oxygen reduction reaction over Pt(111) as a function of applied bias. This allowed us to identify the origin of the overpotential found for this reaction. Adsorbed oxygen and hydroxyl are found to be very stable intermediates at potentials close to equilibrium, and the calculated rate constant for the activated proton/electron transfer to adsorbed oxygen or hydroxyl can account quantitatively for the observed kinetics. On the basis of a database of calculated oxygen and hydroxyl adsorption energies, the trends in the oxygen reduction rate for a large number of different transition and noble metals can be accounted for. Alternative reaction mechanisms involving proton/electron transfer to ...
7,711 citations
"CatMAP: A Software Package for Desc..." refers background or methods in this paper
...;3 þ DE1 þ 0:5ðDE2 þ EO2ðgÞÞ ð6Þ where CO adsorption is assumed to have no barrier, and the relationships from Eqs....
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...For this small set, the accuracy appears to have decreased; however, the discrepancies in the numbers in Table 2 are due to the shortcomings of DFT in calculating gas-phase O2 [35], CO2 [37], and graphite....
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...This can be achieved in a similar way: Energies are given relative to graphite, O2(g), and H2(g) DEa;2 ¼ EO O EO2 2E ) EO O ¼ DEa;2 þ EO2ðgÞ ð5Þ DEa...
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...The experimental gas-phase formation energies are used based on their improved accuracy and the fact that they present a convenient way to apply previously reported corrections for gas-phase CO2 [37] and O2 [35]....
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...2CO2ðgÞ The energies of all relevant species can be calculated using electronic structure methods, or the experimental energies can be found in databases online [32]....
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TL;DR: In this paper, a simple formulation of a generalized gradient approximation for the exchange and correlation energy of electrons has been proposed by Perdew, Burke, and Ernzerhof (PBE), which improves the chemisorption energy of atoms and molecules on transition-metal surfaces.
Abstract: A simple formulation of a generalized gradient approximation for the exchange and correlation energy of electrons has been proposed by Perdew, Burke, and Ernzerhof (PBE) [Phys. Rev. Lett. 77, 3865 (1996)]. Subsequently Zhang and Yang [Phys. Rev. Lett. 80, 890 (1998)] have shown that a slight revision of the PBE functional systematically improves the atomization energies for a large database of small molecules. In the present work, we show that the Zhang and Yang functional (revPBE) also improves the chemisorption energetics of atoms and molecules on transition-metal surfaces. Our test systems comprise atomic and molecular adsorption of oxygen, CO, and NO on Ni(100), Ni(111), Rh(100), Pd(100), and Pd(111) surfaces. As the revPBE functional may locally violate the Lieb-Oxford criterion, we further develop an alternative revision of the PBE functional, RPBE, which gives the same improvement of the chemisorption energies as the revPBE functional at the same time as it fulfills the Lieb-Oxford criterion locally.
5,971 citations
"CatMAP: A Software Package for Desc..." refers background or methods in this paper
...Table 1 shows values calculated with the GPAW code [33] using the RPBE functional [34] (relative to the IUPAC standard states) and values from the CCCBDB [32] (corrected for zero-point energy and thermal enthalpy)....
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...It is well known that DFT performs poorly at calculating the triplet state of O2(g) [35, 36], and the RPBE functional does not include van der Waals forces necessary to describe graphite [34], so these are not ideal choices for reference states....
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01 Jul 1955
TL;DR: A generalization of the inverse of a non-singular matrix is described in this paper as the unique solution of a certain set of equations, which is used here for solving linear matrix equations, and for finding an expression for the principal idempotent elements of a matrix.
Abstract: This paper describes a generalization of the inverse of a non-singular matrix, as the unique solution of a certain set of equations. This generalized inverse exists for any (possibly rectangular) matrix whatsoever with complex elements. It is used here for solving linear matrix equations, and among other applications for finding an expression for the principal idempotent elements of a matrix. Also a new type of spectral decomposition is given.
3,769 citations
Additional excerpts
...C 1⁄4 RDþ ð9Þ where D is the Moore–Penrose pseudo-inverse of D [47, 48]....
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TL;DR: A density functional theory-based, high-throughput screening scheme that successfully uses these strategies to identify a new electrocatalyst for the hydrogen evolution reaction (HER), which is found to have a predicted activity comparable to, or even better than, pure Pt, the archetypical HER catalyst.
Abstract: The pace of materials discovery for heterogeneous catalysts and electrocatalysts could, in principle, be accelerated by the development of efficient computational screening methods. This would require an integrated approach, where the catalytic activity and stability of new materials are evaluated and where predictions are benchmarked by careful synthesis and experimental tests. In this contribution, we present a density functional theory-based, high-throughput screening scheme that successfully uses these strategies to identify a new electrocatalyst for the hydrogen evolution reaction (HER). The activity of over 700 binary surface alloys is evaluated theoretically; the stability of each alloy in electrochemical environments is also estimated. BiPt is found to have a predicted activity comparable to, or even better than, pure Pt, the archetypical HER catalyst. This alloy is synthesized and tested experimentally and shows improved HER performance compared with pure Pt, in agreement with the computational screening results.
3,134 citations
TL;DR: The first steps towards using computational methods to design new catalysts are reviewed and how, in the future, such methods may be used to engineer the electronic structure of the active surface by changing its composition and structure are discussed.
Abstract: Over the past decade the theoretical description of surface reactions has undergone a radical development. Advances in density functional theory mean it is now possible to describe catalytic reactions at surfaces with the detail and accuracy required for computational results to compare favourably with experiments. Theoretical methods can be used to describe surface chemical reactions in detail and to understand variations in catalytic activity from one catalyst to another. Here, we review the first steps towards using computational methods to design new catalysts. Examples include screening for catalysts with increased activity and catalysts with improved selectivity. We discuss how, in the future, such methods may be used to engineer the electronic structure of the active surface by changing its composition and structure.
3,023 citations
"CatMAP: A Software Package for Desc..." refers background in this paper
...The combination of these techniques leads to the ability to predict trends in kinetic properties of heterogeneous catalysts across a range of surfaces using a ‘‘descriptor-based’’ analysis [10, 11]....
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...However, the mean-field model and steady-state solutions have been found to be sufficiently accurate to describe trends in catalysis [10], and can easily and quickly be solved in an automated fashion....
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