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Yamashita T, Miyamura N, Kawai S. Classification of the HCN isomerization reaction dynamics in Ar buffer gas via machine learning. J Chem Phys 2023; 159:124116. [PMID: 38127399 DOI: 10.1063/5.0156313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 09/07/2023] [Indexed: 12/23/2023] Open
Abstract
The effect of the presence of Ar on the isomerization reaction HCN ⇄ CNH is investigated via machine learning. After the potential energy surface function is developed based on the CCSD(T)/aug-cc-pVQZ level ab initio calculations, classical trajectory simulations are performed. Subsequently, with the aim of extracting insights into the reaction dynamics, the obtained reactivity, that is, whether the reaction occurs or not under a given initial condition, is learned as a function of the initial positions and momenta of all the atoms in the system. The prediction accuracy of the trained model is greater than 95%, indicating that machine learning captures the features of the phase space that affect reactivity. Machine learning models are shown to successfully reproduce reactivity boundaries without any prior knowledge of classical reaction dynamics theory. Subsequent analyses reveal that the Ar atom affects the reaction by displacing the effective saddle point. When the Ar atom is positioned close to the N atom (resp. the C atom), the saddle point shifts to the CNH (HCN) region, which disfavors the forward (backward) reaction. The results imply that analyses aided by machine learning are promising tools for enhancing the understanding of reaction dynamics.
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Affiliation(s)
- Takefumi Yamashita
- Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
- Department of Physical Chemistry, School of Pharmacy and Pharmaceutical Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo 142-8501, Japan
| | - Naoaki Miyamura
- Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Shinnosuke Kawai
- Department of Chemistry, Faculty of Science, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
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2
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Vejayan H, Gutiérrez-González A, Torio ME, Busnengo HF, Beck RD. Methylidyne Adsorption on Pt(211) Probed by Reflection Absorption Infrared Spectroscopy (RAIRS). THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2022; 126:20886-20891. [PMID: 36561201 PMCID: PMC9761667 DOI: 10.1021/acs.jpcc.2c07235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/21/2022] [Indexed: 06/17/2023]
Abstract
Methylidyne, CH(ads), adsorbed on a Pt(211) surface and its interaction with chemisorbed hydrogen atoms was studied by reflection absorption infrared spectroscopy (RAIRS). Methylidyne was formed on Pt(211) by methane dissociation from a molecular beam followed by thermal decomposition of the methane dissociation products. CH(ads) was detected by RAIRS via its symmetric C-H stretch vibration resulting in three discrete absorption peaks in the region of 2950-2970 cm-1. While the frequencies of the three C-H stretch peaks remain fixed, their relative intensities depend on the H(ads) co-coverage. This differs markedly from what was observed previously for the RAIR spectra of CH(ads) adsorbed on Pt(111) by the group of Trenary,1 who observed a single C-H stretch peak, which showed a continuous blue shift with increasing H(ads) coverage. Based on our experimental results and density functional theory (DFT) calculations, we propose that the three discrete absorption peaks on Pt(211) are due to the adsorption of methylidyne on the steps of Pt(211) forming one-dimensional rows of adsorbates. Depending on the H(ads) coverage, the CH(ads) species on the step sites can have either zero, one, or two neighboring H(ads) atoms, leading to three different vibrational C-H stretch frequencies and a reversible shift in relative peak intensity depending on the H(ads) coverage.
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Affiliation(s)
- Harmina Vejayan
- Institute
of Chemical Sciences and Engineering (ISIC), École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Ana Gutiérrez-González
- Institute
of Chemical Sciences and Engineering (ISIC), École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - María E. Torio
- Facultad
de Ciencias Exactas, Ingeniería y Agrimensura, Universidad Nacional de Rosario, Avenue Pellegrini 250, 2000 Rosario, Argentina
- Centro
Internacional Franco Argentino de Ciencias de la Información
y de Sistemas (CIFASIS), CONICET-UNR, Boulevard 27 de Febrero 210 bis, 2000 Rosario, Argentina
| | - H. Fabio Busnengo
- Facultad
de Ciencias Exactas, Ingeniería y Agrimensura, Universidad Nacional de Rosario, Avenue Pellegrini 250, 2000 Rosario, Argentina
- Grupo
de Fisicoquímica en Interfaces y Nanoestructuras, Instituto
de Física Rosario (IFIR), CONICET-UNR, Boulevard 27 de Febrero 210 bis, 2000 Rosario, Argentina
| | - Rainer D. Beck
- Institute
of Chemical Sciences and Engineering (ISIC), École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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3
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Pyles CG, Patrow JG, Cheng Y, Tonks IA, Massari AM. Ruthenium hydrides encapsulated in sol–gel glasses exhibit new ultrafast vibrational dynamics. J Chem Phys 2022; 156:124502. [DOI: 10.1063/5.0082752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Vibrational dynamics were measured by IR pump–probe spectroscopy and two-dimensional IR spectroscopy for triruthenium dodecacarbonyl and the undecacarbonyl hydride that forms when it is encapsulated in an alumina sol–gel glass. For comparison, a triruthenium undecacarbonyl hydride salt was also synthesized and studied in neat solution to identify the potential influence of the confined solvent environment on the dynamics experienced by carbon monoxide ligands. The vibrational lifetime was found to be significantly decreased for both hydride species relative to the dodecacarbonyl compound. Conversely, spectral diffusion of the CO vibrations was measured to be faster for the parent compound. The most significant dynamic changes occurred upon transformation from the starting compound to the hydride, while only minor differences were observed between the dynamics of the freely dissolved and sol–gel encapsulated hydrides. The results suggest that the structural change to the hydride has the largest impact on the dynamics and that its improved catalytic properties likely do not originate from confined solvent effects.
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Affiliation(s)
- Cynthia G. Pyles
- University of Minnesota–Twin Cities, 207 Pleasant St. SE, Minneapolis, Minnesota 55454, USA
| | - Joel G. Patrow
- University of Minnesota–Twin Cities, 207 Pleasant St. SE, Minneapolis, Minnesota 55454, USA
| | - Yukun Cheng
- University of Minnesota–Twin Cities, 207 Pleasant St. SE, Minneapolis, Minnesota 55454, USA
| | - Ian A. Tonks
- University of Minnesota–Twin Cities, 207 Pleasant St. SE, Minneapolis, Minnesota 55454, USA
| | - Aaron M. Massari
- University of Minnesota–Twin Cities, 207 Pleasant St. SE, Minneapolis, Minnesota 55454, USA
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4
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Zhou X, Vejayan H, Beck RD, Guo H, Jiang B. Infrared Activities of Adsorbed Species on Metal Surfaces: The Puzzle of Adsorbed Methyl (CH 3). J Phys Chem Lett 2021; 12:11164-11169. [PMID: 34757753 DOI: 10.1021/acs.jpclett.1c03342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Reflection-absorption infrared spectroscopy (RAIRS) is widely used to identify molecular adsorbates on metals during surface chemical reactions, but the interpretation of RAIRS data can be difficult with experiment alone. Here, we reveal from first-principles calculations the origin of the contrasting RAIRS spectra of methyl adsorbed on Pt(111) and Ni(111). We find that the dynamic dipole associated with the symmetric C-H stretch vibration of CH3 along surface normal is significant on Pt(111) but negligibly small on Ni(111), explaining the strong IR activity in the former and the absence of any RAIRS peaks in the latter. This difference is correlated to different charge transfer patterns between metals and the adsorbate, which are determined by the different preferred adsorption sites of methyl on the two surfaces. This work highlights the need of electronic structure calculations in interpreting RAIRS spectra of adsorbates on metal surfaces.
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Affiliation(s)
- Xueyao Zhou
- Hefei National Laboratory for Physical Science at the Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Harmina Vejayan
- Institute of Chemical Sciences and Chemical Engineering (ISIC), École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Rainer D Beck
- Institute of Chemical Sciences and Chemical Engineering (ISIC), École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Hua Guo
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Bin Jiang
- Hefei National Laboratory for Physical Science at the Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
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Auerbach DJ, Tully JC, Wodtke AM. Chemical dynamics from the gas‐phase to surfaces. ACTA ACUST UNITED AC 2021. [DOI: 10.1002/ntls.10005] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Daniel J. Auerbach
- Institut für physikalische Chemie Georg‐August Universität Göttingen Göttingen Germany
- Abteilung für Dynamik an Oberflächen Max‐Planck‐Institut für biophysikalische Chemie Göttingen Germany
| | - John C. Tully
- Department of Chemistry Yale University New Haven Connecticut USA
| | - Alec M. Wodtke
- Institut für physikalische Chemie Georg‐August Universität Göttingen Göttingen Germany
- Abteilung für Dynamik an Oberflächen Max‐Planck‐Institut für biophysikalische Chemie Göttingen Germany
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Kroes GJ. Computational approaches to dissociative chemisorption on metals: towards chemical accuracy. Phys Chem Chem Phys 2021; 23:8962-9048. [PMID: 33885053 DOI: 10.1039/d1cp00044f] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We review the state-of-the-art in the theory of dissociative chemisorption (DC) of small gas phase molecules on metal surfaces, which is important to modeling heterogeneous catalysis for practical reasons, and for achieving an understanding of the wealth of experimental information that exists for this topic, for fundamental reasons. We first give a quick overview of the experimental state of the field. Turning to the theory, we address the challenge that barrier heights (Eb, which are not observables) for DC on metals cannot yet be calculated with chemical accuracy, although embedded correlated wave function theory and diffusion Monte-Carlo are moving in this direction. For benchmarking, at present chemically accurate Eb can only be derived from dynamics calculations based on a semi-empirically derived density functional (DF), by computing a sticking curve and demonstrating that it is shifted from the curve measured in a supersonic beam experiment by no more than 1 kcal mol-1. The approach capable of delivering this accuracy is called the specific reaction parameter (SRP) approach to density functional theory (DFT). SRP-DFT relies on DFT and on dynamics calculations, which are most efficiently performed if a potential energy surface (PES) is available. We therefore present a brief review of the DFs that now exist, also considering their performance on databases for Eb for gas phase reactions and DC on metals, and for adsorption to metals. We also consider expressions for SRP-DFs and briefly discuss other electronic structure methods that have addressed the interaction of molecules with metal surfaces. An overview is presented of dynamical models, which make a distinction as to whether or not, and which dissipative channels are modeled, the dissipative channels being surface phonons and electronically non-adiabatic channels such as electron-hole pair excitation. We also discuss the dynamical methods that have been used, such as the quasi-classical trajectory method and quantum dynamical methods like the time-dependent wave packet method and the reaction path Hamiltonian method. Limits on the accuracy of these methods are discussed for DC of diatomic and polyatomic molecules on metal surfaces, paying particular attention to reduced dimensionality approximations that still have to be invoked in wave packet calculations on polyatomic molecules like CH4. We also address the accuracy of fitting methods, such as recent machine learning methods (like neural network methods) and the corrugation reducing procedure. In discussing the calculation of observables we emphasize the importance of modeling the properties of the supersonic beams in simulating the sticking probability curves measured in the associated experiments. We show that chemically accurate barrier heights have now been extracted for DC in 11 molecule-metal surface systems, some of which form the most accurate core of the only existing database of Eb for DC reactions on metal surfaces (SBH10). The SRP-DFs (or candidate SRP-DFs) that have been derived show transferability in many cases, i.e., they have been shown also to yield chemically accurate Eb for chemically related systems. This can in principle be exploited in simulating rates of catalyzed reactions on nano-particles containing facets and edges, as SRP-DFs may be transferable among systems in which a molecule dissociates on low index and stepped surfaces of the same metal. In many instances SRP-DFs have allowed important conclusions regarding the mechanisms underlying observed experimental trends. An important recent observation is that SRP-DFT based on semi-local exchange DFs has so far only been successful for systems for which the difference of the metal work function and the molecule's electron affinity exceeds 7 eV. A main challenge to SRP-DFT is to extend its applicability to the other systems, which involve a range of important DC reactions of e.g. O2, H2O, NH3, CO2, and CH3OH. Recent calculations employing a PES based on a screened hybrid exchange functional suggest that the road to success may be based on using exchange functionals of this category.
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Affiliation(s)
- Geert-Jan Kroes
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands.
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7
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Abstract
AbstractUnderstanding heterogeneous catalysis at the atomic level requires detailed knowledge of the reactivity of different surface sites toward specific bond breaking and bond making events. We illustrate a new method in such investigations. We use a macroscopically curved Pt single crystal containing a large variation in density of highly kinked steps of two different chiralities. Scanning tunneling microscopy maps the entire range of surface structures present on the 31° section surrounding the Pt(111) apex. Whereas most of the surface shows the expected characteristic arrays of parallel steps, hexagonally-shaped, single-atom deep pits remain after cleaning procedures near the apex. Their orientation is indicative of the different chiralities present on the two sides of the crystal’s apex. These unintended defects locally raise the surface defect concentration, but are of little consequence to subsequent reactivity measurements for $$\text {D}_2$$
D
2
dissociation and H–D exchange as probed by supersonic molecular beam techniques. We quantify absolute elementary dissociation and relative isotopic exchange rates across the surface with high spatial resolution. At low incident energies, elementary dissociation of the homonuclear isotoplogues is dominated by the kinked steps. H–D exchange kinetics depend also mostly linearly on step density. The changing ratio of D2 dissociation to H–D formation, however, suggests that anisotropic diffusion of H(D) atoms is of influence to the measured HD production rate.
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8
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Gutiérrez-González A, Beck RD. Quantum state and surface-site-resolved studies of methane chemisorption by vibrational spectroscopies. Phys Chem Chem Phys 2020; 22:17448-17459. [DOI: 10.1039/d0cp03134h] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Infrared spectroscopic methods enable quantum-state-specific and surface-site-selective studies of methane chemisorption on stepped platinum surfaces.
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Affiliation(s)
- Ana Gutiérrez-González
- Laboratoire de Chimie Physique Moléculaire (LCPM)
- École Polytechnique Fédérale de Lausanne (EPFL)
- CH-1015 Lausanne
- Switzerland
| | - Rainer D. Beck
- Laboratoire de Chimie Physique Moléculaire (LCPM)
- École Polytechnique Fédérale de Lausanne (EPFL)
- CH-1015 Lausanne
- Switzerland
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Gerrits N, Chadwick H, Kroes GJ. Dynamical Study of the Dissociative Chemisorption of CHD 3 on Pd(111). THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2019; 123:24013-24023. [PMID: 31602282 PMCID: PMC6778984 DOI: 10.1021/acs.jpcc.9b05757] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 08/20/2019] [Indexed: 06/10/2023]
Abstract
The specific reaction parameter (SRP) approach to density functional theory has been shown to model reactions of polyatomic molecules with metal surfaces important for heterogeneous catalysis in the industry with chemical accuracy. However, transferability of the SRP functional among systems in which methane interacts with group 10 metals remains unclear for methane + Pd(111). Therefore, in this work, predictions have been made for the reaction of CHD3 on Pd(111) using Born-Oppenheimer molecular dynamics while also performing a rough comparison with experimental data for CH4 + Pd(111) obtained for lower incidence energies. Hopefully, future experiments can test the transferability of the SRP functional among group 10 metals also for Pd(111). We found that the reactivity of CHD3 on Pd(111) is intermediate between and similar to either Pt(111) or Ni(111), depending on the incidence energy and the initial vibrational state distribution. This is surprising because the barrier height and experiments performed at lower incidence energies than investigated here suggest that the reactivity of Pd(111) should be similar to that of Pt(111) only. The relative decrease in the reactivity of Pd(111) at high incidence energies is attributed to site specificity of the reaction and to dynamical effects such as the bobsled effect and energy transfer from methane to the surface.
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Affiliation(s)
- Nick Gerrits
- Gorlaeus
Laboratories, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, the Netherlands
| | - Helen Chadwick
- Department
of Chemistry, Swansea University, Singleton Park, Swansea SA2 8PP, U.K.
| | - Geert-Jan Kroes
- Gorlaeus
Laboratories, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, the Netherlands
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Park GB, Krüger BC, Borodin D, Kitsopoulos TN, Wodtke AM. Fundamental mechanisms for molecular energy conversion and chemical reactions at surfaces. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2019; 82:096401. [PMID: 31304916 DOI: 10.1088/1361-6633/ab320e] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The dream of theoretical surface chemistry is to predict the outcome of reactions in order to find the ideal catalyst for a certain application. Having a working ab initio theory in hand would not only enable these predictions but also provide insights into the mechanisms of surface reactions. The development of theoretical models can be assisted by experimental studies providing benchmark data. Though for some reactions a quantitative agreement between experimental observations and theoretical calculations has been achieved, theoretical surface chemistry is in general still far away from gaining predictive power. Here we review recent experimental developments towards the understanding of surface reactions. It is demonstrated how quantum-state resolved scattering experiments on reactive and nonreactive systems can be used to test front-running theoretical approaches. Two challenges for describing dynamics at surfaces are addressed: nonadiabaticity in diatomic molecule surface scattering and the increasing system size when observing and describing the dynamics of polyatomic molecules at surfaces. Finally recent experimental studies on reactive systems are presented. It is shown how elementary steps in a complex surface reaction can be revealed experimentally.
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Affiliation(s)
- G Barratt Park
- Max Planck Institute for Biophysical Chemistry, Göttingen, Am Fassberg 11, 37077 Göttingen, Germany. Institute for Physical Chemistry, University of Goettingen, Tammannstr. 6, 37077 Göttingen, Germany
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11
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Guo H, Jackson B. Methane dissociation on stepped Ni surfaces resolved by impact site, collision energy, vibrational state, and lattice distortion. J Chem Phys 2019; 150:204703. [DOI: 10.1063/1.5095145] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Han Guo
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA
| | - Bret Jackson
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA
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12
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Jiang B, Guo H. Dynamics in reactions on metal surfaces: A theoretical perspective. J Chem Phys 2019; 150:180901. [PMID: 31091904 DOI: 10.1063/1.5096869] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Recent advances in theoretical characterization of reaction dynamics on metal surfaces are reviewed. It is shown that the widely available density functional theory of metals and their interactions with molecules have enabled first principles theoretical models for treating surface reaction dynamics. The new theoretical tools include methods to construct high-dimensional adiabatic potential energy surfaces, to characterize nonadiabatic processes within the electronic friction models, and to describe dynamics both quantum mechanically and classically. Three prototypical surface reactions, namely, dissociative chemisorption, Eley-Rideal reactions, and recombinative desorption, are surveyed with a focus on some representative examples. While principles governing gas phase reaction dynamics may still be applicable, the presence of the surface introduces a higher level of complexity due to strong interaction between the molecular species and metal substrate. Furthermore, most of these reactive processes are impacted by energy exchange with surface phonons and/or electron-hole pair excitations. These theoretical studies help to interpret and rationalize experimental observations and, in some cases, guide experimental explorations. Knowledge acquired in these fundamental studies is expected to impact many practical problems in a wide range of interfacial processes.
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Affiliation(s)
- Bin Jiang
- Hefei National Laboratory for Physical Science at the Microscale, Department of Chemical Physics, Key Laboratory of Surface and Interface Chemistry and Energy Catalysis of Anhui Higher Education Institutes, University of Science and Technology of China, Hefei 230026, China
| | - Hua Guo
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, USA
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