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Alkyne-Functionalized Cyclooctyne on Si(001): Reactivity Studies and Surface Bonding from an Energy Decomposition Analysis Perspective

ABSTRACT: The reactivity and bonding of an ethinyl-functionalized cyclooctyne on Si(001) is studied by means of density functional theory. This system is promising for the organic functionalization of semiconductors. Singly bonded adsorption structures are obtained by [2 + 2] cycloaddition reactions of the cyclooctyne or ethinyl group with the Si(001) surface. A thermodynamic preference for adsorption with the cyclooctyne group in the on-top position is found and traced back to minimal structural deformation of the adsorbate and surface with the help of energy decomposition analysis for extended systems (pEDA). Starting from singly bonded structures, a plethora of reaction paths describing conformer changes and consecutive reactions with the surface are discussed. Strongly exothermic and exergonic reactions to doubly bonded structures are presented, while small reaction barriers highlight the high reactivity of the studied organic molecule on the Si(001) surface. Dynamic aspects of the competitive bonding of the functional groups are addressed by ab initio molecular dynamics calculations. Several trajectories for the doubly bonded structures are obtained in agreement with calculations using the nudged elastic band approach. However, our findings disagree with the experimental observations of selective adsorption by the cyclooctyne moiety, which is critically discussed.

SUBMITTER: Pieck F

PROVIDER: S-EPMC8586998 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Lithium amides are versatile C-H metallation reagents with vast industrial demand because of their high basicity combined with their weak nucleophilicity, and they are applied in kilotons worldwide annually. The nuclearity of lithium amides, however, modifies and steers reactivity, region- and stereo-selectivity and product diversification in organic syntheses. In this regard, it is vital to understand Li-N bonding as it causes the aggregation of lithium amides to form cubes or ladders from the polar Li-N covalent metal amide bond along the ring stacking and laddering principle. Deaggregation, however, is more governed by the Li←N donor bond to form amine adducts. The geometry of the solid state structures already suggests that there is σ- and π-contribution to the covalent bond. To quantify the mutual influence, we investigated [{(Me2NCH2)2(C4H2N)}Li]2 (1) by means of experimental charge density calculations based on the quantum theory of atoms in molecules (QTAIM) and DFT calculations using energy decomposition analysis (EDA). This new approach allows for the grading of electrostatic Li+N-, covalent Li-N and donating Li←N bonding, and provides a way to modify traditional widely-used heuristic concepts such as the -I and +I inductive effects. The electron density ρ(r) and its second derivative, the Laplacian ∇2ρ(r), mirror the various types of bonding. Most remarkably, from the topological descriptors, there is no clear separation of the lithium amide bonds from the lithium amine donor bonds. The computed natural partial charges for lithium are only +0.58, indicating an optimal density supply from the four nitrogen atoms, while the Wiberg bond orders of about 0.14 au suggest very weak bonding. The interaction energy between the two pincer molecules, (C4H2N)22-, with the Li22+ moiety is very strong (ca. -628 kcal mol-1), followed by the bond dissociation energy (-420.9 kcal mol-1). Partitioning the interaction energy into the Pauli (ΔEPauli), dispersion (ΔEdisp), electrostatic (ΔEelstat) and orbital (ΔEorb) terms gives a 71-72% ionic and 25-26% covalent character of the Li-N bond, different to the old dichotomy of 95 to 5%. In this regard, there is much more potential to steer the reactivity with various substituents and donor solvents than has been anticipated so far.

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Alkyne-Functionalized Cyclooctyne on Si(001): Reactivity Studies and Surface Bonding from an Energy Decomposition Analysis Perspective

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