Search

The chemistry of organic adsorbates on surfaces is often discussed in terms of Pauli repulsion as limiting factor regarding the packing of molecules. Here we show that the attractive part of the van der Waals potential can be similarly decisive. For the semiconductor surface Si(001), an already covalently bonded molecule of cyclooctyne steers a second incoming molecule via dispersion interactions onto the neighbouring adsorption site. This helps in understanding the nonstatistical pattern formation for this surface–adsorbate system and hints toward an inclusion of dispersion attraction as another determining factor for surface adsorption.

Surprising adsorption dynamics in terms of an either direct or pseudodirect pathway in contrast to common precursor-mediated surface reactions is shown for the title system by theoretical investigations. We present a computational protocol for the description of the adsorption dynamics in this complex system that is transferable to other large molecules. The system size prohibits the use of established accurate methods, and approximations have to be made and validated. Our approach combines potential energy surface scans, reaction path determination methods, statistical thermodynamics, and ab initio molecular dynamics simulations based on density functional theory (DFT). This leads to a conclusive picture of adsorption dynamics in the limits of DFT accuracy and shows how a thoughtful selection of methods can comprehensively describe the adsorption dynamics of an experimentally relevant system that might seem too complex for ab initio approaches at first glance.

Wir zeigen mit quantenchemischen Methoden, dass sich die Adsorption von Ether-Molekulen auf Si(001) im Ultrahochvakuum durch klassische Konzepte der organischen Molekulchemie verstehen lasst. Wie unsere detaillierte Analyse zeigt, spiegelt der zweistufige Mechanismus – 1) Ausbildung einer dativen Bindung zwischen dem Sauerstoffatom am Ether und einem Lewis-sauren Oberflachenatom, 2) nukleophiler Angriff eines nahegelegenen Lewis-basischen Oberflachenatoms – die saurekatalysierte Etherspaltung in Losung wider. Zudem ist die dative O-Si-Bindung die starkste ihrer Art und die Reaktivitat in Schritt 2 verlauft entgegen dem Bell-Evans-Polanyi-Prinzip. Mithilfe einer neuartigen Methode der Bindungsanalyse wird auserdem die Umverteilung von Elektronendichte wahrend des C-O-Bindungsbruchs visualisiert. Hierbei wird deutlich, dass der Mechanismus nukleophiler Substitutionen auf Halbleiteroberflachen identisch zu molekularen SN2-Reaktionen ist. Unsere Untersuchungen verdeutlichen, wie die Forschungsfelder der Oberflachenwissenschaften und Molekulchemie voneinander profitieren konnen und so unerwartete Einblicke ermoglichen.

Using computational chemistry, we show that the adsorption of ether molecules on Si(001) under ultra-high vacuum conditions can be understood with textbook organic chemistry. The two-step reaction mechanism of (1) dative bond formation between the ether oxygen and a Lewis acidic surface atom and (2) a nucleophilic attack of a nearby Lewis basic surface atom is analysed in detail and found to mirror the acid-catalysed ether cleavage in solution. The O-Si dative bond is found to be the strongest of its kind and reactivity from this state defies the Bell-Evans-Polanyi principle. Electron rearrangement during the C-O bond cleavage is visualized using a newly developed bonding analysis method, which shows that the mechanism of nucleophilic substitutions on semiconductor surfaces is identical to molecular chemistry SN2 reactions. Our findings thus illustrate how the fields of surface science and molecular chemistry can mutually benefit and unexpected insight can be gained.

The adsorption characteristics of a promising system for hybrid organic-inorganic interfaces, cyclooctyne on Si(001), is analyzed using density functional theory. The chemisorbed 'on-top' configuration, where a cycloadduct is formed between the ring triple bond and a surface dimer, is shown to be most stable. Less stable are 'bridge' and 'sublayer' modes featuring two molecule-surface bonds and the 'pedestal' mode with four bonds. Investigations with our recently proposed periodic energy decomposition analysis (pEDA) reveal that the four-bond configuration is destabilized by large deformation energies needed within molecule and surface as well as rather weak molecule-surface bonds. Dispersion interactions show significant influence on energy and structure of the configurations leading to an increased bending of the rather flexible molecules. Thus, features found in previous scanning tunneling microscopy experiments are conclusively explained with bent 'on-top' configurations and the 'pedestal' mode can be ruled out. A comparison to acetylene shows that the ring structure and the resulting strain of cyclooctyne are responsible for an increased reactivity of the larger adsorbate due to a pre-forming of the ring triple bond for surface bonding. In contrast, ring strain leads only to negligible electronic effects on the adsorbate-surface bonds. The computations highlight the need for in-depth theoretical analysis to understand adsorption characteristics of large, flexible molecules.

Intermediate states to covalent attachment of molecules on surfaces, so called precursors, are usually considered to be physisorbed and mobile. We show that this view should be reconsidered and provide evidence for a chemisorbed precursor for ethylene on Si(001). The character of the molecule-surface bond as a π complex is determined and quantified using our recently developed method for energy and charge analysis in extended systems. In contrast to previous assumptions, the precursor should thus be immobile, which is underlined by computation of high diffusion energy barriers. This has important implications for understanding and modelling of adsorption kinetics. Our analysis highlights that taking the viewpoint of molecular chemistry helps uncover important aspects in the adsorption process on surfaces. Previous experimental results that appear to be in contrast to our model are examined and reinterpreted.

A thorough bonding analysis is performed on the dication [C6(CH3)6SO]2+. The results show that the molecule is best described in terms of covalent interactions between the cations C6(CH3) 6 + and SO+, whereby the bonding consists of two dominating contributions. The strongest bonding comes from dative interaction from the HOMO of C6(CH3) 6 + to the LUMO of SO+, which has overall σ symmetry. The second significant component is due to electron-sharing bonding between the singly occupied orbitals of the two fragments. The bonding situation may be sketched with the formula $$[{\text{C}_{6}}\text{(CH)}_{6}\overrightarrow{-}{\text{SO}}]^{2+}$$ . The bare dication is thermodynamically unstable with regard to dissociation into two cations. It is kinetically stable due to the activation barrier, and it is further stabilized by counterions.

The chemoselective bonding of a bifunctional organic molecule on a semiconductor surface is analyzed with density functional theory (DFT). Periodic energy decomposition analysis is used to reveal the bonding characteristics of different adsorption modes and transition states for 5-ethoxymethyl-5-methylcyclooctyne on Si(001). This system has previously been experimentally proven to be a prototype model system for inorganic–organic hybrid interfaces. The molecule thereby poses challenges for a theoretical description of conformational flexibility and competitive adsorption behavior of the two functional groups. We find that adsorption via the strained triple bond is preferred over the ether group, thus confirming previous experiments. Bonding analysis in combination with static DFT as well as ab initio molecular dynamics methods thereby reveals the determining factors for this chemoselectivity and shows that the functional groups barely influence each other in their surface adsorption.

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.