Bonding character of intermediates in on-surface Ullmann reactions revealed with energy decomposition analysis.

On-surface synthesis has become a thriving topic in surface science. The Ullmann coupling reaction is the most applied synthetic route today, but the nature of the organometallic intermediate is still under discussion. We investigate the bonding nature of prototypical intermediate species (phenyl, naphthyl, anthracenyl, phenanthryl, and triphenylenyl) on the Cu(111) surface with a combination of plane wave and atomic orbital basis set methods using density functional theory calculations with periodic boundary conditions. The surface bonding is shown to be of covalent nature with a polarized shared-electron bond supported by π-back donation effects using energy decomposition analysis for extended systems (pEDA). The bond angle of the intermediates is determined by balancing dispersion attraction and Pauli repulsion between adsorbate and surface. The latter can be significantly reduced by adatoms on the surface. We furthermore investigate how to choose computational parameters for pEDA of organic adsorbates on metal surfaces efficiently and show that bonding interpretation requires consistent choice of the density functional.

Efficient hierarchical models for reactivity of organic layers on semiconductor surfaces.

Computational modeling of organic interface formation on semiconductors poses a challenge to a density functional theory-based description due to structural and chemical complexity. A hierarchical approach is presented, where parts of the interface are successively removed in order to increase computational efficiency while maintaining the necessary accuracy. First, a benchmark is performed to probe the validity of this approach for three model reactions and five dispersion corrected density functionals. Reaction energies are generally well reproduced by generalized gradient approximation-type functionals but accurate reaction barriers require the use of hybrid functionals. Best performance is found for the model system that does not explicitly consider the substrate but includes its templating effects. Finally, this efficient model is used to provide coverage dependent reaction energies and suggest synthetic principles for the prevention of unwanted growth termination reactions for organic layers on semiconductor surfaces.

Click Chemistry in Ultra-high Vacuum - Tetrazine Coupling with Methyl Enol Ether Covalently Linked to Si(001).

The additive-free tetrazine/enol ether click reaction was performed in ultra-high vacuum (UHV) with an enol ether group covalently linked to a silicon surface: Dimethyl 1,2,4,5-tetrazine-3,6-dicarboxylate molecules were coupled to the enol ether group of a functionalized cyclooctyne which was adsorbed on the silicon (001) surface via the strained triple bond of cyclooctyne. The reaction was observed at a substrate temperature of 380 K by means of X-ray photoelectron spectroscopy (XPS). A moderate energy barrier was deduced for this click reaction in vacuum by means of density functional theory based calculations, in good agreement with the experimental results. This UHV-compatible click reaction thus opens a new, flexible route for synthesizing covalently bound organic architectures.

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.

From Acenaphthenes to (+)-Delavatine A: Visible-Light-Induced Ring Closure of Methyl (α-Naphthyl) Acrylates.

Disclosed herein is a visible light mediated cyclization of methyl (α-naphthyl) acrylates and heteroaromatic analogues yielding substituted acenaphthenes and azaacenaphthenes. This highly functional-group-tolerant transformation was put to the test in an enantioselective formal synthesis of delavatine A. Mechanistic details were elucidated by DFT-calculations revealing an unusual intramolecular H-transfer mediated by a primary amine. The generality of this transformation enables a novel synthetic strategy of five membered ring annulation at an advanced stage, allowing reliance upon naphthalene chemistry up to the point of acenaphthene construction.

The Effect of Water and Bases on the Clustering of a Cyclohexene Autoxidation Product C6H8O7 with Sulfuric Acid.

We investigate the molecular interaction between sulfuric acid and a C6H8O7 ketodiperoxy acid compound (a proxy for highly oxidized products of, e.g., monoterpene autoxidation) in the presence of water, ammonia, or dimethylamine. The molecular geometries are obtained using density functional theory (M06-2X, PW91, and ωB97X-D) with the 6-31++G(d,p) basis set, and the binding energy is corrected utilizing a high-level DLPNO-CCSD(T)/def2-QZVPP calculation. The formation free energies were calculated (ΔG at 298 K and 1 atm), and the stability of the molecular clusters was evaluated. The presence of bases is found to enhance the interaction between ketodiperoxy acid compounds and sulfuric acid. The addition of C6H8O7 compounds to (H2SO4)(NH3) or (H2SO4)((CH3)2NH) clusters is, however, not able to compete with the corresponding uptake of another sulfuric acid molecule, even at a high loading of organic compounds. We furthermore investigate the origin of the weak binding of peroxyacid compounds using atoms in molecules and natural bonding orbital analysis. The weak binding is caused by an internal hydrogen bond and the lack of a strong hydrogen bond acceptor in the peroxyacid group. These findings indicate that autoxidation products containing solely or mainly hydroperoxide and carbonyl functional groups do not participate in the initial step of new particle formation and thereby only contribute to the growth of atmospheric particles.

α-Pinene Autoxidation Products May Not Have Extremely Low Saturation Vapor Pressures Despite High O:C Ratios.

COSMO-RS (conductor-like screening model for real solvents) and three different group-contribution methods were used to compute saturation (subcooled) liquid vapor pressures for 16 possible products of ozone-initiated α-pinene autoxidation, with elemental compositions C10H16O4-10 and C20H30O10-12. The saturation vapor pressures predicted by the different methods varied widely. COSMO-RS predicted relatively high saturation vapor pressures values in the range of 10(-6) to 10(-10) bar for the C10H16O4-10 "monomers", and 10(-11) to 10(-16) bar for the C20H30O10-12 "dimers". The group-contribution methods predicted significantly (up to 8 order of magnitude) lower saturation vapor pressures for most of the more highly oxidized monomers. For the dimers, the COSMO-RS predictions were within the (wide) range spanned by the three group-contribution methods. The main reason for the discrepancies between the methods is likely that the group-contribution methods do not contain the necessary parameters to accurately treat autoxidation products containing multiple hydroperoxide, peroxy acid or peroxide functional groups, which form intramolecular hydrogen bonds with each other. While the COSMO-RS saturation vapor pressures for these systems may be overestimated, the results strongly indicate that despite their high O:C ratios, the volatilities of the autoxidation products of α-pinene (and possibly other atmospherically relevant alkenes) are not necessarily extremely low. In other words, while autoxidation products are able to adsorb onto aerosol particles, their evaporation back into the gas phase cannot be assumed to be negligible, especially from the smallest nanometer-scale particles. Their observed effective contribution to aerosol particle growth may therefore involve rapid heterogeneous reactions (reactive uptake) rather than effectively irreversible physical absorption.

The influence of copper on the optical band gap of heterometallic iodido antimonates and bismuthates.

Halogenido metalates of heavy main group elements are versatile semiconductor materials with broad applications. Especially the iodido metalates generally show small optical band gaps, making them suitable for photovoltaics. However, the most promising results have been generated using toxic lead-based materials, raising environmental concerns, while the related and far less toxic bismuth compounds show band gaps too large for direct use in photovoltaics. The introduction of heterometals such as copper can significantly lower the band gap of iodido bismuthates and antimonates, but no clear trend could yet be established in this regard. In this work a short overview over all known copper iodido bismuthates and antimonates is given and this small family of compounds is expanded with nine charged as well as neutral complexes [EkMlIm(P(R)3)n]q- (E = Sb, Bi; M = Cu, Ag; R = Ph, o-tol). The compounds' crystal structures, stability and optical properties are investigated and compared to the findings of quantum chemical investigations. The main excitation is shown to be a copper to antimony or copper to bismuth charge transfer while the relative energetic position of the organic ligand orbitals influences the magnitude of the band gap. This reveals that the nature of the ligands and the coordination environment at the copper atom is crucial for designing new copper iodido antimonates and bismuthates with specific band gaps.

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.

Synthesis of a two-dimensional organic-inorganic bismuth iodide metalate through in situ formation of iminium cations.

(Me2C[double bond, length as m-dash]NMe2)Bi2I7 represents a new layered organic-inorganic iodido bismuthate. It displays an unprecedented anion topology, a low band gap and good stability. Advanced electronic structure analysis finds the II interactions to be decisive for the compound's structural and electronic properties.

Template-controlled on-surface synthesis of a lanthanide supernaphthalocyanine and its open-chain polycyanine counterpart.

Phthalocyanines possess unique optical and electronic properties and thus are widely used in (opto)electronic devices, coatings, photodynamic therapy, etc. Extension of their π-electron systems could produce molecular materials with red-shifted absorption for a broader range of applications. However, access to expanded phthalocyanine analogues with more than four isoindoline units is challenging due to the limited synthetic possibilities. Here, we report the controlled on-surface synthesis of a gadolinium-supernaphthalocyanine macrocycle and its open-chain counterpart poly(benzodiiminoisoindoline) on a silver surface from a naphthalene dicarbonitrile precursor. Their formation is controlled by the on-surface high-dilution principle and steered by different metal templates, i.e., gadolinium atoms and the bare silver surface, which also act as oligomerization catalysts. By using scanning tunneling microscopy, photoemission spectroscopy, and density functional theory calculations, the chemical structures along with the mechanical and electronic properties of these phthalocyanine analogues with extended π-conjugation are investigated in detail.