1
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Ditte M, Barborini M, Medrano Sandonas L, Tkatchenko A. Molecules in Environments: Toward Systematic Quantum Embedding of Electrons and Drude Oscillators. PHYSICAL REVIEW LETTERS 2023; 131:228001. [PMID: 38101380 DOI: 10.1103/physrevlett.131.228001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 07/26/2023] [Accepted: 10/20/2023] [Indexed: 12/17/2023]
Abstract
We develop a quantum embedding method that enables accurate and efficient treatment of interactions between molecules and an environment, while explicitly including many-body correlations. The molecule is composed of classical nuclei and quantum electrons, whereas the environment is modeled via charged quantum harmonic oscillators. We construct a general Hamiltonian and introduce a variational Ansatz for the correlated ground state of the fully interacting molecule-environment system. This wave function is optimized via the variational Monte Carlo method and the ground state energy is subsequently estimated through the diffusion Monte Carlo method. The proposed scheme allows an explicit many-body treatment of electrostatic, polarization, and dispersion interactions between the molecule and the environment. We study solvation energies and excitation energies of benzene derivatives, obtaining excellent agreement with explicit ab initio calculations and experiments.
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Affiliation(s)
- Matej Ditte
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg City, Luxembourg
| | - Matteo Barborini
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg City, Luxembourg
| | - Leonardo Medrano Sandonas
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg City, Luxembourg
| | - Alexandre Tkatchenko
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg City, Luxembourg
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2
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Jones LO, Mosquera MA, Schatz GC, Ratner MA. Embedding Methods for Quantum Chemistry: Applications from Materials to Life Sciences. J Am Chem Soc 2020; 142:3281-3295. [PMID: 31986877 DOI: 10.1021/jacs.9b10780] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Quantum mechanical embedding methods hold the promise to transform not just the way calculations are performed, but to significantly reduce computational costs and improve scaling for macro-molecular systems containing hundreds if not thousands of atoms. The field of embedding has grown increasingly broad with many approaches of different intersecting flavors. In this perspective, we lay out the methods into two streams: QM:MM and QM:QM, showcasing the advantages and disadvantages of both. We provide a review of the literature, the underpinning theories including our contributions, and we highlight current applications with select examples spanning both materials and life sciences. We conclude with prospects and future outlook on embedding, and our view on the use of universal test case scenarios for cross-comparisons of the many available (and future) embedding theories.
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Affiliation(s)
- Leighton O Jones
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , United States
| | - Martín A Mosquera
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , United States
| | - George C Schatz
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , United States
| | - Mark A Ratner
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , United States
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3
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Kick M, Oberhofer H. Towards a transferable design of solid-state embedding models on the example of a rutile TiO2 (110) surface. J Chem Phys 2019; 151:184114. [DOI: 10.1063/1.5125204] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- M. Kick
- Chair for Theoretical Chemistry and Catalysis Research Center, Technical University of Munich, Lichtenbergstr. 4, 85747 Garching, Germany
| | - H. Oberhofer
- Chair for Theoretical Chemistry and Catalysis Research Center, Technical University of Munich, Lichtenbergstr. 4, 85747 Garching, Germany
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4
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Theoretical study of O2 interaction with subnanometer-sized Ag clusters supported on defective SiO2 surface. COMPUT THEOR CHEM 2018. [DOI: 10.1016/j.comptc.2018.10.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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5
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Aal SA. Adsorption of NO on Pd and Pd2 supported at the regular and defective CdO (0 0 1) surfaces: Density functional theory study. JOURNAL OF TAIBAH UNIVERSITY FOR SCIENCE 2018. [DOI: 10.1016/j.jtusci.2013.09.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Safa A. Aal
- Department of Chemistry, Faculty of Science and Arts, Qassim University, PO Box 6666, Qassim, Buraidah, Saudi Arabia
- Department of Chemistry, Faculty of Science, Benha University, PO Box 13518, Benha, Egypt
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6
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Chulhai DV, Goodpaster JD. Projection-Based Correlated Wave Function in Density Functional Theory Embedding for Periodic Systems. J Chem Theory Comput 2018; 14:1928-1942. [DOI: 10.1021/acs.jctc.7b01154] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Dhabih V. Chulhai
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455, United States
| | - Jason D. Goodpaster
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455, United States
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7
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Liu Y, Wang Q, Liu H, Li K, Jia L, Li D, Hou B, Wang B. Insights into the metal-support interaction between NiCu cluster and MgO as well as its effect on H adsorption and H2 dissociation. MOLECULAR CATALYSIS 2017. [DOI: 10.1016/j.mcat.2017.04.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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8
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Ivanova-Shor EA, Shor AM, Laletina SS, Deka RC, Nasluzov VA. Modeling of heterogeneous catalysts based on silica and zeolites by the hybrid quantum chemical embedded cluster method. Russ Chem Bull 2017. [DOI: 10.1007/s11172-017-1808-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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9
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Huang C. Patching the Exchange-Correlation Potential in Density Functional Theory. J Chem Theory Comput 2016; 12:2224-33. [DOI: 10.1021/acs.jctc.6b00051] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Chen Huang
- Department
of Scientific
Computing, Florida State University, Tallahassee, Florida 32306-4120, United States
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10
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Buendía F, Vargas JA, Beltrán MR, Davis JBA, Johnston RL. A comparative study of AumRhn (4 ≤ m + n ≤ 6) clusters in the gas phase versus those deposited on (100) MgO. Phys Chem Chem Phys 2016; 18:22122-8. [DOI: 10.1039/c6cp03735f] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The combined use of a genetic algorithm and Density Functional Theory (DFT) calculations allows us to explore the potential energy surface. Our results show interesting effects on the geometries of the clusters on deposition. Two-dimensional clusters in the gas phase become three-dimensional and vice versa.
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Affiliation(s)
- Fernando Buendía
- Instituto de Investigaciones en Materiales
- Universidad Nacional Autónoma de México
- México D.F
- Mexico
| | - Jorge A. Vargas
- Instituto de Investigaciones en Materiales
- Universidad Nacional Autónoma de México
- México D.F
- Mexico
| | - Marcela R. Beltrán
- Instituto de Investigaciones en Materiales
- Universidad Nacional Autónoma de México
- México D.F
- Mexico
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11
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Soini TM, Rösch N. Size-dependent properties of transition metal clusters: from molecules to crystals and surfaces--computational studies with the program ParaGauss. Phys Chem Chem Phys 2015; 17:28463-83. [PMID: 26456800 DOI: 10.1039/c5cp04281j] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
In the so-called scalable regime the size-dependent behavior of the physical and chemical properties of transition metal clusters is described by scaling relationships. For most quantities this scalable regime is reached for cluster sizes between a few tens and a few hundreds of atoms, hence for systems for which an accurate treatment by density functional theory is still feasible. Thus, by invoking scaling relations one is able to obtain properties of very large nanoparticles and even the bulk limit from the results of a series of smaller cluster models. In this invited review we illustrate this strategy by exploiting results from computational studies that mostly were carried out with the density functional theory software ParaGauss. We address mainly the size-dependent behavior of the properties of transition metal clusters. To this end, we first present benchmark studies probing various approximations that are used in such density functional calculations. Subsequently we show how physical insight may be gained by exploring less understood types of systems. These applications range from bare clusters to nanoislands and nanoalloys to adsorption complexes.
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Affiliation(s)
- Thomas M Soini
- Department Chemie and Catalysis Research Center, Technische Universität München, 85747 Garching, Germany.
| | - Notker Rösch
- Department Chemie and Catalysis Research Center, Technische Universität München, 85747 Garching, Germany. and Institute of High Performance Computing, Agency for Science, Technology and Research, 1 Fusionopolis Way, Connexis #16-16, Singapore 138632, Singapore
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12
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Nasluzov VA, Parker SM, Genest A, Shor AM, Ivanova-Shor EA, Rösch N. Trinuclear tantalum clusters grafted to hydroxylated silica surfaces: A density-functional embedded-cluster study. KINETICS AND CATALYSIS 2015. [DOI: 10.1134/s0023158415050134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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13
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Heard CJ, Heiles S, Vajda S, Johnston RL. Pd(n)Ag(4-n) and Pd(n)Pt(4-n) clusters on MgO (100): a density functional surface genetic algorithm investigation. NANOSCALE 2014; 6:11777-11788. [PMID: 25158024 DOI: 10.1039/c4nr03363a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The novel surface mode of the Birmingham Cluster Genetic Algorithm (S-BCGA) is employed for the global optimisation of noble metal tetramers upon an MgO (100) substrate at the GGA-DFT level of theory. The effect of element identity and alloying in surface-bound neutral subnanometre clusters is determined by energetic comparison between all compositions of PdnAg(4-n) and PdnPt(4-n). While the binding strengths to the surface increase in the order Pt > Pd > Ag, the excess energy profiles suggest a preference for mixed clusters for both cases. The binding of CO is also modelled, showing that the adsorption site can be predicted solely by electrophilicity. Comparison to CO binding on a single metal atom shows a reversal of the 5σ-d activation process for clusters, weakening the cluster-surface interaction on CO adsorption. Charge localisation determines homotop, CO binding and surface site preferences. The electronic behaviour, which is intermediate between molecular and metallic particles allows for tunable features in the subnanometre size range.
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Affiliation(s)
- Christopher J Heard
- Department of Applied Physics, Chalmers University of Technology, SE 412-96 Gothenburg, Sweden
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14
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Bendavid LI, Carter EA. Status in Calculating Electronic Excited States in Transition Metal Oxides from First Principles. Top Curr Chem (Cham) 2014; 347:47-98. [DOI: 10.1007/128_2013_503] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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15
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Brinkmann L, Heifets E, Kantorovich L. Density functional calculations of extended, periodic systems using Coulomb corrected molecular fractionation with conjugated caps method (CC-MFCC). Phys Chem Chem Phys 2014; 16:21252-70. [DOI: 10.1039/c3cp55119a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A consistent DFT based formulation of the order-N molecular fractionation with conjugated caps method in which a molecular system is calculated considering a set of finite fragments, is proposed. Here we apply the method and test its performance on a periodic metal–organic framework system.
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Affiliation(s)
| | - Eugene Heifets
- Max Planck Institute for Solid State Research
- D-70569 Stuttgart, Germany
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16
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Sousa C, Tosoni S, Illas F. Theoretical Approaches to Excited-State-Related Phenomena in Oxide Surfaces. Chem Rev 2012. [DOI: 10.1021/cr300228z] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Carmen Sousa
- Departament de Química
Física and Institut de Química Teòrica i Computacional
(IQTCUB), Universitat de Barcelona, C/Martí
i Franquès 1, 08028 Barcelona, Spain
| | - Sergio Tosoni
- Departament de Química
Física and Institut de Química Teòrica i Computacional
(IQTCUB), Universitat de Barcelona, C/Martí
i Franquès 1, 08028 Barcelona, Spain
- Departamento de Química, Universidad de Las Palmas de Gran Canaria, Campus Universitario
de Tafira, 35017 Las Palmas de Gran Canaria, Spain
| | - Francesc Illas
- Departament de Química
Física and Institut de Química Teòrica i Computacional
(IQTCUB), Universitat de Barcelona, C/Martí
i Franquès 1, 08028 Barcelona, Spain
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17
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Theoretical Modelling of Oxide-Supported Metal Nanoclusters and Nanoalloys. ACTA ACUST UNITED AC 2012. [DOI: 10.1016/b978-0-08-096357-0.00003-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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18
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Keal TW, Sherwood P, Dutta G, Sokol AA, Catlow CRA. Characterization of hydrogen dissociation over aluminium-doped zinc oxide using an efficient massively parallel framework for QM/MM calculations. Proc Math Phys Eng Sci 2011. [DOI: 10.1098/rspa.2010.0613] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A task-farm parallelization framework has been implemented in the ChemShell computational chemistry environment to provide a facility for parallelizing common chemical calculations, including finite-difference Hessian evaluation, the nudged elastic band method for reaction path optimization, and population-based methods for global optimization. The optimization methods are provided by a parallel interface to the DL-FIND optimization library. As ChemShell can already exploit parallel external programs for energy and gradient evaluations, the new methods result in a two-level approach to parallelization that gives significantly improved performance for massively parallel calculations. For typical systems, speed-up factors of five to eight times have been observed compared with non-task-farmed calculations. The task-farming version of ChemShell has been used to study the heterolytic dissociation of a hydrogen molecule over a polar oxygen-terminated surface of aluminium-doped zinc oxide using an embedded cluster hybrid QM/MM approach. We calculate a 42 kcal mol
−1
heat of reaction and a 30 kcal mol
−1
activation energy, which is equivalent to a high backward reaction barrier of 72 kcal mol
−1
per H
2
molecule, in close agreement with temperature programmed desorption experiments. The dissociation path includes a stable intermediate comprising a hydride ion in an oxygen vacancy and physisorbed atomic hydrogen.
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Affiliation(s)
- Thomas W. Keal
- Computational Science and Engineering Department, STFC Daresbury Laboratory, Daresbury, Warrington WA4 4AD, UK
| | - Paul Sherwood
- Computational Science and Engineering Department, STFC Daresbury Laboratory, Daresbury, Warrington WA4 4AD, UK
| | - Gargi Dutta
- Department of Chemistry, University College London, Kathleen Lonsdale Materials Chemistry, 20 Gordon Street, London WC1H 0AJ, UK
| | - Alexey A. Sokol
- Department of Chemistry, University College London, Kathleen Lonsdale Materials Chemistry, 20 Gordon Street, London WC1H 0AJ, UK
| | - C. Richard A. Catlow
- Department of Chemistry, University College London, Kathleen Lonsdale Materials Chemistry, 20 Gordon Street, London WC1H 0AJ, UK
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19
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Nasluzov VA, Ivanova-Shor EA, Shor AM, Yudanov IV, Rösch N. Simulation of heterogeneous catalysts and catalytic processes using the density functional method. KINETICS AND CATALYSIS 2010. [DOI: 10.1134/s0023158410060091] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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20
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Abstract
Abstract
We overview quantum mechanical simulations that model the adsorption of actinide ions at solvated mineral surfaces. Pertinent examples illustrate the status of this emerging field of computational chemistry. In particular, we describe our own studies on uranyl adsorption on kaolinite. Already the few available results, from applications of density functional methods to cluster models or periodic slab models, show that such calculations are a useful complement to experimental investigations. Detailed information at the atomic level from accurate electronic structure calculations on well defined model systems helps to refine current interpretations of the chemical nature of uranyl adsorption species and to discover new features of these interface systems. Results from quantum mechanical simulations also provide a valuable reference for future experimental investigations.
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21
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Bär M, Faber B, Reinhard PG, Dinh PM, Suraud E, Wopperer P. Dynamics of Na clusters in/on insulating substrates. ACTA ACUST UNITED AC 2010. [DOI: 10.1088/1742-6596/248/1/012023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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22
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Small gold species at hydroxylated alumina surfaces. A computational study using embedded-cluster models of α-Al2O3(0001). Chem Phys Lett 2010. [DOI: 10.1016/j.cplett.2010.06.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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23
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Shor AM, Shor EAI, Laletina S, Nasluzov VA, Vayssilov GN, Rösch N. Effect of the size of the quantum region in a hybrid embedded-cluster scheme for zeolite systems. Chem Phys 2009. [DOI: 10.1016/j.chemphys.2009.07.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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24
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He J, Di Paola C, Kantorovich L. Partitioning scheme for density functional calculations of extended systems. J Chem Phys 2009; 130:144104. [DOI: 10.1063/1.3106661] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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25
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Harding JH, Duffy DM, Sushko ML, Rodger PM, Quigley D, Elliott JA. Computational Techniques at the Organic−Inorganic Interface in Biomineralization. Chem Rev 2008; 108:4823-54. [DOI: 10.1021/cr078278y] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- John H. Harding
- Department of Engineering Materials, University of Sheffield, Sheffield, U.K
| | | | | | | | | | - James A. Elliott
- Department of Materials Science and Metallurgy, University of Cambridge, Cambridge, U.K
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26
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Huang P, Carter EA. Advances in correlated electronic structure methods for solids, surfaces, and nanostructures. Annu Rev Phys Chem 2008; 59:261-90. [PMID: 18031211 DOI: 10.1146/annurev.physchem.59.032607.093528] [Citation(s) in RCA: 128] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Calculations of the electronic structure of solids began decades ago, but only recently have solid-state quantum techniques become sufficiently reliable that their application is nearly as routine as quantum chemistry is for molecules. We aim to introduce chemists to the pros and cons of first-principles methods that can provide atomic-scale insight into the properties and chemistry of bulk materials, interfaces, and nanostructures. The techniques we review include the ubiquitous density functional theory (DFT), which is often sufficient, especially for metals; extensions such as DFT + U and hybrid DFT, which incorporate exact exchange to rid DFT of its spurious self-interactions (critical for some semiconductors and strongly correlated materials); many-body Green's function (GW and Bethe-Salpeter) methods for excited states; quantum Monte Carlo, in principle an exact theory but for which forces (hence structure optimization and dynamics) are problematic; and embedding theories that locally refine the quantum treatment to improve accuracy.
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Affiliation(s)
- Patrick Huang
- Department of Mechanical and Aerospace Engineering and Program in Applied and Computational Mathematics, Princeton University, Princeton, New Jersey 08544-5263, USA
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27
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Ramo DM, Shluger AL. Structure and spectroscopic properties of oxygen divacancy in yttrium-stabilized zirconia. ACTA ACUST UNITED AC 2008. [DOI: 10.1088/1742-6596/117/1/012022] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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28
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Zhang Y, Lin H. Flexible-Boundary Quantum-Mechanical/Molecular-Mechanical Calculations: Partial Charge Transfer between the Quantum-Mechanical and Molecular-Mechanical Subsystems. J Chem Theory Comput 2008; 4:414-25. [DOI: 10.1021/ct700296x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yan Zhang
- Chemistry Department, University of Colorado Denver, Denver, Colorado 80217-3364
| | - Hai Lin
- Chemistry Department, University of Colorado Denver, Denver, Colorado 80217-3364
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29
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Sterrer M, Risse T, Giordano L, Heyde M, Nilius N, Rust HP, Pacchioni G, Freund HJ. Palladium-Monomere, -Dimere und -Trimere auf der MgO(001)-Oberfläche: Betrachtung einzelner Cluster. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200702444] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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30
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Shor AM, Shor EAI, Nasluzov VA, Vayssilov GN, Rösch N. First Hybrid Embedding Scheme for Polar Covalent Materials Using an Extended Border Region To Minimize Boundary Effects on the Quantum Region. J Chem Theory Comput 2007; 3:2290-300. [DOI: 10.1021/ct700159k] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alexei M. Shor
- Institute of Chemistry and Chemical Technology, Russian Academy of Sciences, 660049 Krasnoyarsk, Russian Federation, Faculty of Chemistry, University of Sofia, 1126 Sofia, Bulgaria, and Department Chemie, Technische Universität München, 85747 Garching, Germany
| | - Elena A. Ivanova Shor
- Institute of Chemistry and Chemical Technology, Russian Academy of Sciences, 660049 Krasnoyarsk, Russian Federation, Faculty of Chemistry, University of Sofia, 1126 Sofia, Bulgaria, and Department Chemie, Technische Universität München, 85747 Garching, Germany
| | - Vladimir A. Nasluzov
- Institute of Chemistry and Chemical Technology, Russian Academy of Sciences, 660049 Krasnoyarsk, Russian Federation, Faculty of Chemistry, University of Sofia, 1126 Sofia, Bulgaria, and Department Chemie, Technische Universität München, 85747 Garching, Germany
| | - Georgi N. Vayssilov
- Institute of Chemistry and Chemical Technology, Russian Academy of Sciences, 660049 Krasnoyarsk, Russian Federation, Faculty of Chemistry, University of Sofia, 1126 Sofia, Bulgaria, and Department Chemie, Technische Universität München, 85747 Garching, Germany
| | - Notker Rösch
- Institute of Chemistry and Chemical Technology, Russian Academy of Sciences, 660049 Krasnoyarsk, Russian Federation, Faculty of Chemistry, University of Sofia, 1126 Sofia, Bulgaria, and Department Chemie, Technische Universität München, 85747 Garching, Germany
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31
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Sterrer M, Risse T, Giordano L, Heyde M, Nilius N, Rust HP, Pacchioni G, Freund HJ. Palladium Monomers, Dimers, and Trimers on the MgO(001) Surface Viewed Individually. Angew Chem Int Ed Engl 2007; 46:8703-6. [DOI: 10.1002/anie.200702444] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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32
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Di Valentin C, Neyman KM, Risse T, Sterrer M, Fischbach E, Freund HJ, Nasluzov VA, Pacchioni G, Rösch N. Density-functional model cluster studies of EPR g tensors of Fs+ centers on the surface of MgO. J Chem Phys 2007; 124:044708. [PMID: 16460201 DOI: 10.1063/1.2161190] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We report g tensors of surface color centers, so-called F(s) (+) centers, of MgO calculated with two density-functional approaches using accurately embedded cluster models. In line with recent UHV measurements on single-crystalline MgO film, we determined only small g-tensor anisotropies and negative shifts Deltag identical with g-g(e) for all F(s) (+) sites considered, namely, (001)-terrace, step, edge, and corner sites. The g values are very sensitive to the local structure of the defect: relaxation reverses the sign of Deltag. However, accounting for the spin-orbit interaction either self-consistently or perturbatively yields very similar results. In addition to the values of the tensor components, their direction with respect to the surface was determined. In contrast to edges, significant deviations from ideal C(2v) symmetry were found for F(s) (+) centers at steps. Recent data on single-crystalline thin films are reevaluated in the light of these results.
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Affiliation(s)
- Cristiana Di Valentin
- Dipartimento di Scienza dei Materiali, Università degli Studi Milano-Bicocca, 20125 Milano, Italy
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Barcaro G, Aprà E, Fortunelli A. Structure of Ag Clusters Grown on Fs-Defect Sites of an MgO(1 0 0) Surface. Chemistry 2007; 13:6408-18. [PMID: 17497620 DOI: 10.1002/chem.200601796] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The structure of AgN clusters (N=1-4, 6, 8, 10), both in the gas phase and grown on the MgO(1 0 0) surface containing Fs-defects, has been investigated by a density functional basin-hopping (DF-BH) approach. In analogy with what observed in the case of gold clusters, it is found that the presence of the defect implies a double frustration and a cylindrical invariance of the metal-surface interaction, causing small Ag clusters growing around the Fs defect to be highly fluxional. Nevertheless, two different structural crossovers are found to be induced by the metal-defect interaction for the adsorbed clusters such that: 1) planar structures prevail for N<or=4 (as in the gas phase); 2) noncrystalline (fivefold symmetric) structures, which are the lowest energy ones in the gas phase for medium sized AgN clusters (N>or=7), prevail for N=6 and N=8; 3) distorted face-centered cubic (fcc) structures grown pseudomorphically on the defected surface prevail for N=10. The transition from fivefold to fcc motifs is rationalized in terms of the double-frustration effect, which increases the bond strain of the noncrystalline structures. Detrapping energies from the defect were also calculated; the lowest energy pathway corresponds to the detachment of a dimer.
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Affiliation(s)
- Giovanni Barcaro
- Molecular Modeling Laboratory, IPCF-CNR, Via G. Moruzzi 1, Pisa, 56124, Italy
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Zhang Y, Lin H, Truhlar DG. Self-Consistent Polarization of the Boundary in the Redistributed Charge and Dipole Scheme for Combined Quantum-Mechanical and Molecular-Mechanical Calculations. J Chem Theory Comput 2007; 3:1378-98. [DOI: 10.1021/ct7000107] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yan Zhang
- Chemistry Department, University of Colorado at Denver and Health Sciences Center, Denver, Colorado 80217-3364, and Chemistry Department and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431
| | - Hai Lin
- Chemistry Department, University of Colorado at Denver and Health Sciences Center, Denver, Colorado 80217-3364, and Chemistry Department and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431
| | - Donald G. Truhlar
- Chemistry Department, University of Colorado at Denver and Health Sciences Center, Denver, Colorado 80217-3364, and Chemistry Department and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431
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Bosko SI, Moskaleva LV, Matveev AV, Rösch N. Optical Spectra of Cu, Ag, and Au Monomers and Dimers at Regular Sites and Oxygen Vacancies of the MgO(001) Surface. A Systematic Time-Dependent Density Functional Study Using Embedded Cluster Models. J Phys Chem A 2007; 111:6870-80. [PMID: 17477512 DOI: 10.1021/jp070303g] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Polarization-resolved optical spectra of coinage metal monomers and dimers Mn (M=Cu, Ag, Au; n=1, 2) at ideal O2- sites of MgO(001) as well as at oxygen vacancies, Fs and Fs+, of that surface were established using a computational approach based on linear response time-dependent density functional theory. Calculations were performed for structures determined by applying a generalized-gradient density functional method to cluster models embedded in an elastic polarizable environment. This embedding scheme provides an accurate description of substrate relaxation and long-range electrostatic interaction. We compared the optical properties of adsorbed atoms and dimers with those of the corresponding gas-phase species and we systematically analyzed trends among congeners.
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Affiliation(s)
- Sergey I Bosko
- Department Chemie, Technische Universität München, 85747 Garching, Germany
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Chizallet C, Costentin G, Che M, Delbecq F, Sautet P. Infrared Characterization of Hydroxyl Groups on MgO: A Periodic and Cluster Density Functional Theory Study. J Am Chem Soc 2007; 129:6442-52. [PMID: 17465545 DOI: 10.1021/ja068720e] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The infrared OH stretching frequencies of the various types of hydroxyl groups on MgO surfaces have been calculated by periodic (VASP) and cluster (Gaussian) DFT simulations. Surface irregularities (mono and diatomic steps, corners, step divacancies, and kinks) have been considered to model the IR spectra of hydroxylated MgO powders. A good correspondence between calculated and experimental frequencies is obtained with the B3LYP functional. Hydrogen-bonding is the parameter which influences most the IR frequency of OH groups, followed by location of OH groups in concave or convex areas of the surface and then oxygen coordination. The evolution of experimental IR spectra upon evacuation at increasing temperature can be rationalized on the basis of calculated thermal stabilities of each kind of OH groups. A new model is finally proposed to help assign the experimental bands, in terms of hydrogen-bonding, local topology of the hydroxylated sites, and coordination of oxygen.
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Affiliation(s)
- Céline Chizallet
- Laboratoire de Réactivité de Surface, Université Pierre et Marie Curie-Paris 6, CNRS 4 place Jussieu, 75252 Paris Cedex 05, France.
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Cinquini F, Valentin CD, Finazzi E, Giordano L, Pacchioni G. Theory of oxides surfaces, interfaces and supported nano-clusters. Theor Chem Acc 2006. [DOI: 10.1007/s00214-006-0204-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Neyman KM, Inntam C, Moskaleva LV, Rösch N. Density Functional Embedded Cluster Study of Cu4, Ag4and Au4Species Interacting with Oxygen Vacancies on the MgO(001) Surface. Chemistry 2006; 13:277-86. [PMID: 16969882 DOI: 10.1002/chem.200600545] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cu(4), Ag(4), and Au(4) species adsorbed on an MgO(001) surface that exhibits neutral (F(s)) and charged (F(s) (+)) oxygen vacancies have been studied using a density functional approach and advanced embedding models. The gas-phase rhombic-planar structure of the coinage metal tetramers is only moderately affected by adsorption. In the most stable surface configuration, the plane of the tetramers is oriented perpendicular to the MgO(001) surface; one metal atom is attached to an oxygen vacancy and another one is bound to a nearby surface oxygen anion. A very similar structural motif was recently found on defect-free MgO(001), where two O(2-) ions serve as adsorption sites. Following the trend of the interactions with the regular MgO(001) surface, Au(4) and Cu(4) bind substantially stronger to F(s) and F(s) (+) sites than Ag(4). This stronger adsorption interaction at oxygen vacancies, in particular at F(s), is partly due to a notable accumulation of electron density on the adsorbates. We also examined the propensity of small supported metal species to aggregate to adsorbed di-, tri- and tetramers. Furthermore, we demonstrated that core-level ionization potentials offer the possibility for detecting experimentally supported metal tetramers and characterizing them structurally with the help of calculated data.
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Affiliation(s)
- Konstantin M Neyman
- ICREA, 08010 Barcelona and Departament de Química Física, Universitat de Barcelona, 08028 Barcelona, Spain.
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39
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Di Valentin C, Neyman KM, Risse T, Sterrer M, Fischbach E, Freund HJ, Nasluzov VA, Pacchioni G, Rösch N. Density-functional model cluster studies of EPR g tensors of Fs+ centers on the surface of MgO. J Chem Phys 2006. [DOI: 10.1063/1.2161190 10.1063/1.2161190] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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41
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Inntam C, Moskaleva LV, Yudanov IV, Neyman KM, Rösch N. Adsorption of Cu4, Ag4 and Au4 particles on the regular MgO(001) surface: A density functional study using embedded cluster models. Chem Phys Lett 2006. [DOI: 10.1016/j.cplett.2005.10.080] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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42
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Neyman KM, Inntam C, Matveev AV, Nasluzov VA, Rösch N. Single d-Metal Atoms on Fs and Fs+ Defects of MgO(001): A Theoretical Study across the Periodic Table. J Am Chem Soc 2005; 127:11652-60. [PMID: 16104741 DOI: 10.1021/ja052437i] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Single d-metal atoms on oxygen defects F(s) and F(s+) of the MgO(001) surface were studied theoretically. We employed an accurate density functional method combined with cluster models, embedded in an elastic polarizable environment, and we applied two gradient-corrected exchange-correlation functionals. In this way, we quantified how 17 metal atoms from groups 6-11 of the periodic table (Cu, Ag, Au; Ni, Pd, Pt; Co, Rh, Ir; Fe, Ru, Os; Mn, Re; and Cr, Mo, W) interact with terrace sites of MgO. We found bonding with F(s) and F(s+) defects to be in general stronger than that with O2- sites, except for Mn-, Re-, and Fe/F(s) complexes. In M/F(s) systems, electron density is accumulated on the metal center in a notable fashion. The binding energy on both kinds of O defects increases from 3d- to 4d- to 5d-atoms of a given group, at variance with the binding energy trend established earlier for the M/O2- complexes, 4d < 3d < 5d. Regarding the evolution of the binding energy along a period, group 7 atoms are slightly destabilized compared to their group 6 congeners in both the F(s) and F(s+) complexes; for later transition elements, the binding energy increases gradually up to group 10 and finally decreases again in group 11, most strongly on the F(s) site. This trend is governed by the negative charge on the adsorbed atoms. We discuss implications for an experimental detection of metal atoms on oxide supports based on computed core-level energies.
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44
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45
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Formation of Pd dimers at regular and defect sites of the MgO(100) surface: cluster model calculations. Chem Phys 2005. [DOI: 10.1016/j.chemphys.2004.02.022] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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46
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Ménétrey M, Markovits A, Minot C, Pacchioni G. Formation of Schottky Defects at the Surface of MgO, TiO2, and SnO2: A Comparative Density Functional Theoretical Study. J Phys Chem B 2004. [DOI: 10.1021/jp048497c] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- M. Ménétrey
- Laboratoire de Chimie Théorique, Université P. et M. Curie, 4 Place Jussieu case 137, 75252 Paris Cedex 05, France
| | - A. Markovits
- Laboratoire de Chimie Théorique, Université P. et M. Curie, 4 Place Jussieu case 137, 75252 Paris Cedex 05, France
| | - C. Minot
- Laboratoire de Chimie Théorique, Université P. et M. Curie, 4 Place Jussieu case 137, 75252 Paris Cedex 05, France
| | - G. Pacchioni
- Dipartimento di Scienza dei Materiali, Università di Milano-Bicocca,Via R. Cozzi, 53-20125 Milano, Italy
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Herschend B, Baudin M, Hermansson K. A combined molecular dynamics+quantum mechanics method for investigation of dynamic effects on local surface structures. J Chem Phys 2004; 120:4939-48. [PMID: 15267356 DOI: 10.1063/1.1635802] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A combined molecular dynamics (MD)+quantum mechanics (QM) method for studying processes on ionic surfaces is presented. Through the combination of classical MD and ab initio embedded-cluster calculations, this method allows the modeling of surface processes involving both the structural and dynamic features of the substrate, even for large-scale systems. The embedding approach used to link the information from the MD simulation to the cluster calculation is presented, and rigorous tests have been carried out to ensure the feasibility of the method. The electrostatic potential and electron density resulting from our embedded-cluster model have been compared with periodic slab results, and confirm the satisfying quality of our embedding scheme as well as the importance of applying embedding in our combined MD+QM approach. We show that a highly accurate representation of the Madelung potential becomes a prerequisite when the embedded-cluster approach is applied to temperature-distorted surface snapshots from the MD simulation.
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Affiliation(s)
- Bjorn Herschend
- Department of Materials Chemistry, The Angstrom Laboratory, Uppsala University, Box 538, S-751 21 Uppsala, Sweden
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48
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Giordano L, Di Valentin C, Goniakowski J, Pacchioni G. Nucleation of Pd dimers at defect sites of the MgO(100) surface. PHYSICAL REVIEW LETTERS 2004; 92:096105. [PMID: 15089494 DOI: 10.1103/physrevlett.92.096105] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2003] [Indexed: 05/24/2023]
Abstract
Point defects on oxide surfaces are presumed to be preferential nucleation sites for supported metal clusters. Under typical growth conditions, dimers constitute the first step in island nucleation. First-principles calculations on the formation of Pd dimers on regular and defect sites of the MgO(100) surface show that nucleation occurs with large dimer binding energies at divacancies and charged oxygen vacancies (F+ centers), while it is less favorable on steps and neutral F centers. The extensive database of defect trapping/attachment properties gives a firm basis to rationalize recent atomic-force microscopy findings and provides guidelines valid, in general, for ionic substrates.
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Affiliation(s)
- Livia Giordano
- Dipartimento di Scienza dei Materiali, Università di Milano-Bicocca, Istituto Nazionale per la Fisica della Materia, Via R. Cozzi, 53, 20125, Milano, Italy
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Rösch N, Matveev A, Nasluzov VA, Neyman KM, Moskaleva L, Krüger S. Quantum chemistry with the Douglas-Kroll-Hess approach to relativistic density functional theory: Efficient methods for molecules and materials. THEORETICAL AND COMPUTATIONAL CHEMISTRY 2004. [DOI: 10.1016/s1380-7323(04)80038-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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50
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Abstract
Crystalline solids and surfaces have become a subject of growing interest. The difficulty of a comprehensive description of a variety of phenomena by a single method has led to the development of many models. These models can be classified as nonperiodic and periodic models. The former include free clusters, saturated clusters, and embedded clusters. The latter two models serve to remove the boundary effects of the free clusters. No perfect avoidance of such effects can be achieved in this way. The cyclic cluster model overcomes this difficulty in a natural way. It is periodic with a finite periodicity. An embedding can take into account a long-range effect in ionic crystals. Previous periodic approaches relied on the large unit cell model, which is related to the supercell approach. For perfect crystals the conventional unit cell approach is a well-known standard. However, its disadvantage is the unphysical periodicity of defects, which is avoided in the cyclic cluster model. The present article presents a description of these models together with selective applications to solid-state systems and surfaces.
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Affiliation(s)
- Karl Jug
- Theoretische Chemie, Universität Hannover, Am Kleinen Felde 30, 30167 Hannover, Germany.
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