Ethers on Si(001): A Prime Example for the Common Ground between Surface Science and Molecular Organic Chemistry

Chemoselective Adsorption of Allyl Ethers on Si(001): How the Interaction between Two Functional Groups Controls the Reactivity and Final Products of a Surface Reaction

Selective adsorption of multifunctional molecules is rarely observed when the different functional groups react via nonactivated reaction channels. Although the latter is also the case for ether cleavage and the adsorption of C=C double bonds on the highly reactive Si(001) surface, we find that allyl ethers, which combine both functional groups, react on Si(001) selectively via the cleavage of the molecules' ether group. In addition, our XPS measurements at 90, 150, and 300 K indicate an increased reactivity of the ether group when compared to monofunctional ethers. STM investigations furthermore reveal different final adsorption configurations after ether cleavage of allyl methyl ether when compared to diethyl ether as the monofunctional reference molecule. The interaction of the two functional groups in one molecule thus leads to new reaction channels with higher reactivity for ether cleavage on Si(001). As a further consequence, the reactivity of the C=C double bond is suppressed up to room temperature, leading to the observed selective adsorption.

Decoding energy decomposition analysis: Machine-learned Insights on the impact of the density functional on the bonding analysis

The concept of chemical bonding is a crucial aspect of chemistry that aids in understanding the complexity and reactivity of molecules and materials. However, the interpretation of chemical bonds can be hindered by the choice of the theoretical approach and the specific method utilized. This study aims to investigate the effect of choosing different density functionals on the interpretation of bonding achieved through energy decomposition analysis (EDA). To achieve this goal, a data set was created, representing four bonding groups and various combinations of functionals and dispersion correction schemes. The calculations showed significant variation among the different functionals for the EDA terms, with the dispersion correction terms exhibiting the highest variability. More information was extracted by using machine learning in combination with dimensionality reduction on the data set. Results indicate that, despite the differences in the EDA terms obtained from different functionals, the functional has the least significant impact, suggesting minimal influence on the bonding interpretation.

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

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.

Surface functionalization with nonalternant aromatic compounds: a computational study of azulene and naphthalene on Si(001)

Nonalternant aromatic π-electron systems show promises for surface functionalization due to their unusual electronic structure. Based on our previous experiences for metal surfaces, we investigate the adsorption structures, adsorption dynamics and bonding characteristics of azulene and its alternant aromatic isomer naphthalene on the Si(001) surface. Using a combination of density functional theory,ab initiomolecular dynamics, reaction path sampling and bonding analysis with the energy decomposition analysis for extended systems, we show that azulene shows direct adsorption paths into several, strongly bonded chemisorbed final structures with up to four covalent carbon-silicon bonds which can be described in a donor-acceptor and a shared-electron bonding picture nearly equivalently. Naphthalene also shows these tetra-σ-type bonding structures in accordance with an earlier study. But the adsorption path is pseudo-direct here with a precursor intermediate bonded via one aromatic ring and strong indications for a narrow adsorption funnel. The four surface-adsorbate bonds formed lead for both adsorbates to a strong corrugation and a loss of aromaticity.

Adsorption dynamics of bifunctional molecules: Allyl methyl ether on Si(001)

The reaction dynamics of allyl methyl ether (AME) on Si(001) was studied by means of molecular beam techniques. The reaction of this bifunctional molecule comprising an ether and an alkene group was found to proceed via an intermediate state as deduced from the temperature dependence of the initial sticking probability s₀. At constant surface temperature T_s, s₀ decreases continuously with increasing kinetic energy E_kin, indicating a non-activated adsorption channel. Qualitatively and quantitatively, the energy dependence is almost identical to the adsorption dynamics of diethyl ether on Si(001). We attribute this to a similar nature of the intermediate state, which largely determines the adsorption dynamics. In consequence, this indicates a predominant role of the ether group and a minor influence of the C=C double bond on the adsorption dynamics of AME on Si(001).

Combined XPS and DFT investigation of the adsorption modes of methyl enol ether functionalized cyclooctyne on Si(001)

The reaction of methyl enol ether functionalized cyclooctyne on the silicon (001) surface was investigated by means of X‐ray photoelectron spectroscopy (XPS) and density functional theory (DFT). Three different groups of final states were identified; all of them bind on Si(001) via the strained triple bond of cyclooctyne but they differ in the configuration of the methyl enol ether group. The majority of molecules adsorbs without additional reaction of the enol ether group; the relative contribution of this configuration to the total coverage depends on substrate temperature and coverage. Further configurations include enol ether groups which reacted on the silicon surface either via ether cleavage or enol ether groups which transformed on the surface into a carbonyl group.

Complementary Base Lowers the Barrier in SuFEx Click Chemistry for Primary Amine Nucleophiles

The sulfur(VI) fluoride exchange (SuFEx) reaction is an emerging scheme for connecting molecular building blocks. Due to its broad functional group tolerance and rather stable resulting linkage, it is seeing rapid adoption in various fields of chemistry. Still, to date the reaction mechanism is poorly understood, which hampers further development. Here, we show that the mechanism of the SuFEx reaction for the prototypical example of methanesulfonyl fluoride reacting with methylamine can be understood as an SN2-type reaction. By analyzing the reaction path with the help of density functional theory in vacuo and under consideration of solvent and co-reactant influence, we identify the often used complementary base as a crucial ingredient to lower the reaction barrier significantly by increasing the nucleophilicity of the primary amine. With the help of energy decomposition analysis at the transition state structures, we quantify the underlying stereoelectronic effects and propose new avenues for experimental exploration of the potential of SuFEx chemistry.

Parameter-free coordination numbers for solutions and interfaces

Coordination numbers are among the central quantities to describe the local environment of atoms and are thus used in various applications such as structure analysis, fingerprints, and parameters. Yet, there is no consensus regarding a practical algorithm, and many proposed methods are designed for specific systems. In this work, we propose a scale-free and parameter-free algorithm for nearest neighbor identification. This algorithm extends the powerful Solid-Angle based Nearest-Neighbor (SANN) framework to explicitly include local anisotropy. As such, our Anisotropically corrected SANN (ASANN) algorithm provides with a fast, robust, and adaptive method for computing coordination numbers. The ASANN algorithm is applied to flat and corrugated metallic surfaces to demonstrate that the expected coordination numbers are retrieved without the need for any system-specific adjustments. The same applies to the description of the coordination numbers of metal atoms in AuCu nanoparticles, and we show that ASANN based coordination numbers are well adapted for automatically counting neighbors and the establishment of cluster expansions. Analysis of classical molecular dynamics simulations of an electrified graphite electrode reveals a strong link between the coordination number of Cs⁺ ions and their position within the double layer, a relation that is absent for Na⁺, which keeps its first solvation shell even close to the electrode.

Dynamics of proton transfer reactions on silicon surfaces: OH-dissociation of methanol and water on Si(001)

The reaction dynamics of methanol and water on Si(001) were investigated by means of molecular beam techniques. The initial sticking probability s₀ was determined as a function of the kinetic energy of the incoming molecules, E_kin, and surface temperature, T_s. For both, methanol and water, a nonactivated reactional channel was observed; the dynamics were found to be determined by the reaction into the datively bonded intermediate state. A low conversion barrier was deduced for the conversion from this intermediate into the final state. It is attributed to the reaction mechanism, which proceeds via proton transfer from the OH-group of the datively bonded molecules to a Si surface atom. Despite this low conversion barrier, adsorption into the intermediate and further reaction via proton transfer were found to be largely decoupled.

Bond Insertion at Distorted Si(001) Subsurface Atoms

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.

Site-selective reversible Diels–Alder reaction between a biphenylene-based polyarene and a semiconductor surface

A multidisciplinary study reveals the chemistry of a polycyclic conjugated molecule on a Ge(001):H surface.