Chemisorption of a Strained but Flexible Molecule: Cyclooctyne on Si(001)

Pecher, Lisa; Schober, Christoph; Tonner, Ralf

doi:10.1002/chem.201605952

Cited by 26 publications

(88 citation statements)

References 53 publications

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“…The dispersion interaction term is computed from the prepared fragments to be consistent with the other energy terms in the pEDA. It thus deviates from the usual dispersion interaction term computed via the supermolecular approach . The actual EDA procedure then decomposes Δ E int (elec) into contributions from Pauli repulsion, electrostatics (elstat) and orbital interaction (orb):

Δ E_{int} ((), elec) = Δ E_{Pauli} + Δ E_{elstat} + Δ E_{orb}

…”

Section: Methodsmentioning

confidence: 96%

Deriving bonding concepts for molecules, surfaces, and solids with energy decomposition analysis for extended systems

Pecher

Tonner

2018

WIREs Comput Mol Sci

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Chemical bonding concepts like covalency, ionicity, Pauli repulsion, shared-electron, or donor-acceptor bonding are important tools to sort our vast knowledge in chemistry and predict new reactivity. Electronic structure analysis provides the basis for a detailed understanding of the origins of these concepts. Energy decomposition analysis (EDA) is an established method for molecules and has recently been implemented for application in extended systems, that is, surfaces and solids, where it is termed periodic EDA (pEDA). The foundations and applications of this method which enables the derivation of bonding concepts are outlined in this review. Embedded in key examples from molecular and solid-state chemistry, the major part covers the adsorption and reactivity of molecules with surfaces with a focus on organic molecules interacting with semiconductor surfaces. Based on electronic structure analysis and supported by a quantitative methodology, we show that analogous bonding concepts can be applied in diverse chemical environments. This article is categorized under: Electronic Structure Theory > Ab Initio Electronic Structure Methods Structure and Mechanism > Computational Materials Science K E Y W O R D S chemical bonding, density functional theory, energy decomposition analysis, surface chemistry 1 | INTRODUCTIONThe chemical bond is the central concept in the discussion of structures and reactivity in chemistry. The nature of the forces that hold atoms together thrills chemists since the upcoming of atomistic theories. First realistic models were derived more than two centuries ago based on experimental observations. 1 The paradigm shift at the beginning of the 20th century then provided the basis for our present-day understanding of chemical bonding in terms of quantum mechanical principles. 2,3 But by no means did this development end the discussion about chemical bonding and the interpretation of results obtained by theory and computation. The intrinsic ambiguity in discussing often nonobservable properties that are connected to very useful concepts like covalency, ionicity, Pauli repulsion, bond order, and alike fosters the scientific discussion and leads to a further refinement of our understanding of the chemical bond. [4][5][6][7][8][9][10][11] The development of bonding concepts in molecular and solid-state chemistry evolved separately for the most part. For molecules, the view on (more or less) localized bonds as given by the Lewis picture more than a century ago 12 was regained both by valence bond (VB) theory and from the molecular orbital (MO) approach by the linear combination of atomic orbitals (LCAO) and localization procedures. [13][14][15][16] This resulted in the development of many powerful methods for electronic structure analysis for the qualitative and quantitative interpretation of chemical bonding that have been summarized in previous reviews. 2,17-21 Some examples will be discussed in the next section. In the field of surfaces and solids, the delocalized view

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Δ E_{int} ((), elec) = Δ E_{Pauli} + Δ E_{elstat} + Δ E_{orb}

…”

Section: Methodsmentioning

confidence: 96%

Deriving bonding concepts for molecules, surfaces, and solids with energy decomposition analysis for extended systems

Pecher

Tonner

2018

WIREs Comput Mol Sci

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“…An alternative idea would be to assume that the reaction is under thermodynamic control. This also does not deliver a coherent picture, since all theoretical studies predict the on-top mode to be more stable than bridge at low coverage [20,21,30,35,57]. Therefore, a new, presumably more complex model of the adsorption dynamics must be devised, which we cannot provide at this moment.…”

Section: Comparison With Experimentsmentioning

confidence: 92%

“…In the c direction, a vacuum layer of at least 10 Å was ensured. Convergence studies on these parameters can be found in a previous work [57]. The bonding energy E bond was defined as the difference between the energy E tot of the relaxed total system and the energies E surf and E mol of the relaxed and isolated surface and molecule:…”

Section: Surfacesmentioning

confidence: 99%

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Bond Insertion at Distorted Si(001) Subsurface Atoms

Pecher

Tonner

2018

Inorganics

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Using density functional theory (DFT) methods, we analyze the adsorption of acetylene and ethylene on the Si(001) surface in an unusual bond insertion mode. The insertion takes place at a saturated tetravalent silicon atom and the insight gained can thus be transferred to other saturated silicon compounds in molecular and surface chemistry. Molecular orbital analysis reveals that the distorted and symmetry-reduced coordination of the silicon atoms involved due to surface reconstruction raises the electrophilicity and, additionally, makes certain σ bond orbitals more accessible. The affinity towards bond insertion is, therefore, caused by the structural constraints of the surface. Additionally, periodic energy decomposition analysis (pEDA) is used to explain why the bond insertion structure is much more stable for acetylene than for ethylene. The increased acceptor abilities of acetylene due to the presence of two π*-orbitals (instead of one π*-orbital and a set of σ*(C-H) orbitals for ethylene), as well as the lower number of hydrogen atoms, which leads to reduced Pauli repulsion with the surface, are identified as the main causes. While our findings imply that this structure might be an intermediate in the adsorption of acetylene on Si(001), the predicted product distributions are in contradiction to the experimental findings. This is critically discussed and suggestions to resolve this issue are given.

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“…[8][9][10][11] As one of the few examples, Tonner and co-workers have demonstrated that EDAs on semi-conducting surfaces can provide a deep understanding of coverage effects 12 and elucidate peculiar bonding mechanisms. 13 Our goal is to extend the EDA based on the block-localized wave function (BLW) 14,15 to metallic surfaces. The BLW is designed to localize the electrons in Hilbert space in the Mulliken sense, i.e., in terms of atom-centered basis functions.…”

Section: Introductionmentioning

confidence: 99%

Energy Decomposition Analysis for Metal Surface–Adsorbate Interactions by Block Localized Wave Functions

Staub

Iannuzzi

Khaliullin

et al. 2018

J. Chem. Theory Comput.

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The energy decomposition analysis based on block localized wave functions (BLW-EDA) allows to gain physical insight into the nature of chemical bonding, decomposing the interaction energy in (1) a "frozen" term, accounting for the attraction due to electrostatic and dispersion interactions, modulated by Pauli repulsion, (2) the variationally assessed polarization energy and (3) the charge-transfer. This method has so far been applied to gas-and condensed-phase molecular systems. However, its standard version is not compatible with fractionally occupied orbitals (i.e. electronic smearing) and, as a consequence, cannot be applied to metallic surfaces. In this work, we propose a 1 simple and practical extension of BLW-EDA to fractionally occupied orbitals, termed Ensemble BLW-EDA. As illustrative examples, we have applied the developed method to analyze the nature of the interaction of various adsorbates on Pt(111), ranging from physisorbed water to strongly chemisorbed ethylene. Our results show that polarization and charge-transfer both contribute significantly at the adsorption minimum for all studied systems. The energy decomposition analysis provides details with respect to competing adsorption sites (e.g., CO on atop, vs. hollow sites) and elucidates the respective importance of polarization and charge transfer for the increased adsorption energy of H 2 S compared to H 2 O. Our development will enable a deeper understanding of the impact of charge transfer on catalytic processes in general.

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Chemisorption of a Strained but Flexible Molecule: Cyclooctyne on Si(001)

Cited by 26 publications

References 53 publications

Deriving bonding concepts for molecules, surfaces, and solids with energy decomposition analysis for extended systems

Deriving bonding concepts for molecules, surfaces, and solids with energy decomposition analysis for extended systems

Bond Insertion at Distorted Si(001) Subsurface Atoms

Energy Decomposition Analysis for Metal Surface–Adsorbate Interactions by Block Localized Wave Functions

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