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.

Relevance of π-Backbonding for the Reactivity of Electrophilic Anions [B12 X11 ]- (X=F, Cl, Br, I, CN).

Electrophilic anions of type [B12 X11 ]- posses a vacant positive boron binding site within the anion. In a comparatitve experimental and theoretical study, the reactivity of [B12 X11 ]- with X=F, Cl, Br, I, CN is characterized towards different nucleophiles: (i) noble gases (NGs) as σ-donors and (ii) CO/N2 as σ-donor-π-acceptors. Temperature-dependent formation of [B12 X11 NG]- indicates the enthalpy order (X=CN)>(X=Cl)≈(X=Br)>(X=I)≈(X=F) almost independent of the NG in good agreement with calculated trends. The observed order is explained by an interplay of the electron deficiency of the vacant boron site in [B12 X11 ]- and steric effects. The binding of CO and N2 to [B12 X11 ]- is significantly stronger. The B3LYP 0 K attachment enthapies follow the order (X=F)>(X=CN)>(X=Cl)>(X=Br)>(X=I), in contrast to the NG series. The bonding motifs of [B12 X11 CO]- and [B12 X11 N2 ]- were characterized using cryogenic ion trap vibrational spectroscopy by focusing on the CO and N2 stretching frequencies ν C O and ν N 2 , respectively. Observed shifts of ν C O and ν N 2 are explained by an interplay between electrostatic effects (blue shift), due to the positive partial charge, and by π-backdonation (red shift). Energy decomposition analysis and analysis of natural orbitals for chemical valence support all conclusions based on the experimental results. This establishes a rational understanding of [B12 X11 ]- reactivety dependent on the substituent X and provides first systematic data on π-backdonation from delocalized σ-electron systems of closo-borate anions.

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.

Solvent-Induced Bond-Bending Isomerism in Hexaphenyl Carbodiphosphorane: Decisive Dispersion Interactions in the Solid State.

Previous reports in the literature describe that the crystallization of hexaphenyl carbodiphosphorane (CDPPh) from a variety of solvents gives a "bent" geometry for the P-C-P moiety as the solid-state molecular structure. However, a linear structure is observed when CDPPh is crystallized from benzene. Here, we report detailed spectroscopic and theoretical studies on the linear and bent structures. X-ray powder diffraction examinations show a phase transition of linear CDPPh upon the loss of co-crystallized benzene molecules, which is accompanied by the bending of the P-C-P unit. Studies on the linear and bent structures (i.e., X-ray powder diffraction, solid-state NMR, UV-vis spectroscopy, and IR spectroscopy) show significant differences in their properties. Investigations of the solid-state structures with density functional theory-based methods (PBE-D3) point toward subtle dispersion effects being responsible for this solvent-induced bond-bending isomerism in CDPPh.

[{(PhSn)3SnS6}{(MCp)3S4}] (M = W, Mo): Minimal Molecular Models of the Covalent Attachment of Metal Chalcogenide Clusters on Doped Transition Metal Dichalcogenide Layers.

With the aim to mimic the yet unknown covalent deposition of metal chalcogenide clusters on transition metal dichalcogenide (TMDC) MoS2 or WS2 layers, and thereby explore the interaction between the two systems and potential consequences on physical properties of the TMDC material, we synthesized heterobimetallic model systems. The heterocubane-type cluster [(SnCl3)(WCp)3S4] (1), the organotin-sulfidomolybdate cluster [{(PhSn)3SnS6}{(MoCp)3S4}] (2), and the corresponding tungstate [(PhSn)3SnS6{(WCp)3S4}] (3) were obtained in ligand exchange reactions from [(PhSn)4S6] and [M(CO)3CpCl]. Indeed, the {M3S4} cages in 1-3 resemble a section of the respective TMDC monolayers, altogether representing minimal molecular model systems for the adsorption of organotin sulfide clusters on MoS2 or WS2. The interaction between the {(MCp)3S4} and {(PhSn)3SnS6} subunits is characterized by multicenter bonding, rendering the respective Sn atom as Sn(II), hence driving the clusters into a mixed-valence Sn(IV)/Sn(II) situation, and the M atoms as M(IV) upon an in situ redox process. The attachment is thus weaker than via regular covalent M-S bonds, but definitely stronger than via van der Waals interactions that have been characteristic for all known interactions of clusters on TMDC surfaces so far. Computational analyses of an extended model mimicking the electronic situation in the cluster prove the analogy to a covalent attachment on TMDCs.

Conditional Singlet Oxygen Generation through a Bioorthogonal DNA-targeted Tetrazine Reaction.

We report the use of bioorthogonal reactions as an original strategy in photodynamic therapy to achieve conditional phototoxicity and specific subcellular localization simultaneously. Our novel halogenated BODIPY-tetrazine probes only become efficient photosensitizers (ΦΔ ≈0.50) through an intracellular inverse-electron-demand Diels-Alder reaction with a suitable dienophile. Ab initio computations reveal an activation-dependent change in decay channels that controls 1 O2 generation. Our bioorthogonal approach also enables spatial control. As a proof-of-concept, we demonstrate the feasibility of the selective activation of our dormant photosensitizer in cellular nuclei, causing cancer cell death upon irradiation. Thus, our dual biorthogonal, activatable photosensitizers open new venues to combat current limitations of photodynamic therapy.

Comparison of the periodic slab approach with the finite cluster description of metal-organic interfaces at the example of PTCDA on Ag(110).

We present a comparative study of metal-organic interface properties obtained from dispersion corrected density functional theory calculations based on two different approaches: the periodic slab-supercell technique and cluster models with 32-290 Ag atoms. Fermi smearing and fixing of cluster borders are required to make the cluster calculation feasible and realistic. The considered adsorption structure and energy of a PTCDA molecule on the Ag(110) surface is not well reproduced with clusters containing only two metallic layers. However, all clusters with four layers of silver atoms and sufficient lateral extension reproduce the adsorbate structure within 0.04 Å with respect to the slab-supercell structure and provide adsorption energies of ( -4.45± 0.08 eV) consistent with the slab result of -4.47 eV. Thus, metal-organic adsorbate systems can be realistically represented by properly defined cluster models. © 2018 Wiley Periodicals, Inc.

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.

Ternary Iodido Bismuthates and the Special Role of Copper.

Two new, isostructural members of the title material class, [PPh4]4[Cu2Bi2I12] (1) and [PPh4]4[Ag2Bi2I12] (2), have been prepared via a facile solution route. The crystal structure of both compounds features a tetranuclear [M2Bi2I12]4- (M = Cu, Ag) anion that displays an unprecedented face-sharing mode of connection between BiI6 octahedra and MI4 tetrahedra, enabling close Bi···M contacts. The two compounds allow for a direct experimental and quantum chemical investigation of the influence of group 11 metal cations on the optical and electronic properties of ternary iodido bismuthate anions, indicating that Cu+ is a better electronic match than Ag+, resulting in a significantly lower optical band gap of the copper compound.

An experimental and computational study on isomerically pure, soluble azaphthalocyanines and their complexes and boron azasubphthalocyanines of a varying number of aza units.

Herein, we present a series of isomerically pure, peripherally alkyl substituted, soluble and low aggregating azaphthalocyanines as well as their new, smaller hybrid homologues, azasubphthalocyanines. The focus lies on the effect of the systematically increasing number of aza building blocks [-N[double bond, length as m-dash]] replacing the non-peripheral [-CH[double bond, length as m-dash]] units and their influence on the physical and photophysical properties of these chromophores. The absolute and relative HOMO-LUMO energies of azaphthalocyanines were analyzed using UV-Vis and CV and compared to the density functional theory calculations (B3LYP, TD-DFT). The lowering of the HOMO level is revealed as the determining factor for the trend in the adsorption energies by electronic structure analysis. Crystals of substituted subphthalocyanines, N2-Pc*H2 and N4-[Pc*Zn·H2O], were obtained out of DCM. For the synthesis of the valuable tetramethyltetralin phthalocyanine building block a new highly efficient synthesis involving a nearly quantitative CoII catalyzed aerobic autoxidation step is introduced replacing inefficient KMnO4/pyridine as the oxidant.

Dispersion-mediated steering of organic adsorbates on a precovered silicon surface.

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.

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

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.

Precursor States of Organic Adsorbates on Semiconductor Surfaces are Chemisorbed and Immobile.

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.

Site-Specific Reactivity of Ethylene at Distorted Dangling-Bond Configurations on Si(001).

Differences in adsorption and reaction energetics for ethylene on Si(001) are reported with respect to distorted dangling-bond configurations induced by hydrogen precoverage, as obtained by DFT calculations. This can help to understand the influence of surface defects and precoverage on the reactivity of organic molecules on semiconductor surfaces in general. The results show that the reactivity of surface dimers fully enclosed by hydrogen-covered atoms is essentially unchanged compared to the clean surface. This is confirmed by scanning tunneling microscopy measurements. On the contrary, adsorption sites with partially covered surface dimers show a drastic increase in reactivity. This is due to a lowering of the reaction barrier by more than 50 % relative to the clean surface, which is in line with previous experiments. Adsorption on dimers enclosed by molecule (ethylene)-covered surface atoms is reported to have a strongly decreased reactivity, as a result of destabilization of the intermediate state due to steric repulsion; this is quantified through periodic energy decomposition analysis. Furthermore, an approach for the calculation of Gibbs energies of adsorption based on statistical thermodynamics considerations is applied to the system. The results show that the loss in molecular entropy leads to a significant destabilization of adsorption states.

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

By using computational chemistry it has been shown that the adsorption of ether molecules on Si(001) under ultrahigh vacuum conditions can be understood with classical concepts of organic chemistry. Detailed analysis of the two-step reaction mechanism-1) formation of a dative bond between the ether oxygen atom and a Lewis acidic surface atom and 2) nucleophilic attack of a nearby Lewis basic surface atom-shows that it mirrors acid-catalyzed ether cleavage in solution. The O-Si dative bond is the strongest of its kind, and the reactivity in step 2 defies the Bell-Evans-Polanyi principle. Electron rearrangement during C-O bond cleavage has been visualized with a newly developed method for analyzing bonding, which shows that the mechanism of nucleophilic substitutions on semiconductor surfaces is identical to molecular SN 2 reactions. Our findings illustrate how surface science and molecular chemistry can mutually benefit from each other and unexpected insight can be gained.

From small fullerenes to the graphene limit: A harmonic force-field method for fullerenes and a comparison to density functional calculations for Goldberg-Coxeter fullerenes up to C980.

We introduce a simple but computationally very efficient harmonic force field, which works for all fullerene structures and includes bond stretching, bending, and torsional motions as implemented into our open-source code Fullerene. This gives accurate geometries and reasonably accurate vibrational frequencies with root mean square deviations of up to 0.05 Šfor bond distances and 45.5 cm(-1) for vibrational frequencies compared with more elaborate density functional calculations. The structures obtained were used for density functional calculations of Goldberg-Coxeter fullerenes up to C980. This gives a rather large range of fullerenes making it possible to extrapolate to the graphene limit. Periodic boundary condition calculations using density functional theory (DFT) within the projector augmented wave method gave an energy difference between -8.6 and -8.8 kcal/mol at various levels of DFT for the reaction C60 →graphene (per carbon atom) in excellent agreement with the linear extrapolation to the graphene limit (-8.6 kcal/mol at the Perdew-Burke-Ernzerhof level of theory).

Lewis Acids as Activators in CBS-Catalysed Diels-Alder Reactions: Distortion Induced Lewis Acidity Enhancement of SnCl4.

The effect of several Lewis acids on the CBS catalyst (named after Corey, Bakshi and Shibata) was investigated in this study. While (2) H NMR spectroscopic measurements served as gauge for the activation capability of the Lewis acids, in situ FT-IR spectroscopy was employed to assess the catalytic activity of the Lewis acid oxazaborolidine complexes. A correlation was found between the Δδ((2) H) values and rate constants kDA , which indicates a direct translation of Lewis acidity into reactivity of the Lewis acid-CBS complexes. Unexpectedly, a significant deviation was found for SnCl4 as Lewis acid. The SnCl4 -CBS adduct was much more reactive than the Δδ((2) H) values predicted and gave similar reaction rates to those observed for the prominent AlBr3 -CBS adduct. To rationalize these results, quantum mechanical calculations were performed. The frontier molecular orbital approach was applied and a good correlation between the LUMO energies of the Lewis acid-CBS-naphthoquinone adducts and kDA could be found. For the SnCl4 -CBS-naphthoquinone adduct an unusual distortion was observed leading to an enhanced Lewis acidity. Energy decomposition analysis with natural orbitals for chemical valence (EDA-NOCV) calculations revealed the relevant interactions and activation mode of SnCl4 as Lewis acid in Diels-Alder reactions.

Surface Chemistry of tert-Butylphosphine (TBP) on Si(001) in the Nucleation Phase of Thin-Film Growth.

We combine density functional theory calculations and scanning tunneling microscopy investigations to identify the relevant chemical species and reactions in the nucleation phase of chemical vapor deposition. tert-Butylphosphine (TBP) was deposited on a silicon substrate under conditions typical for surface functionalization and growth of semiconductor materials. On the activated hydrogen-covered surface H/Si(001) it forms a strong covalent P-Si bond without loss of the tert-butyl group. Calculations show that site preference for multiple adsorption of TBP is influenced by steric repulsion of the adsorbate's bulky substituent. STM imaging furthermore revealed an anisotropic distribution of TBP with a preference for adsorption perpendicular to the surface dimer rows. The adsorption patterns found can be understood by a mechanism invoking stabilization of surface hydrogen vacancies through electron donation by an adsorbate. The now improved understanding of nucleation in thin-film growth may help to optimize molecular precursors and experimental conditions and will ultimately lead to higher quality materials.

Molecular structure and vibrations of NTCDA monolayers on Ag(111) from density-functional theory and infrared absorption spectroscopy.

The structure and vibrational properties of the metal-organic interface of 1,4,5,8-naphthalene-tetracarboxylic dianhydride (NTCDA) on Ag(111) were analysed using Fourier-transform infrared absorption spectroscopy in conjunction with density functional theory calculations including dispersion forces (PBE-D3). Mode assignments and polarizations as well as molecular distortions were determined for four adsorption geometries of NTCDA on top and bridge sites aligned either parallel or perpendicular to the Ag rows and compared to accurate calculations of the free molecule. This enables an in-depth understanding of surface effects on the computed and experimental vibrational spectra of the adsorbed NTCDA molecule. The molecule-substrate interaction comprises two major and equally important contributions: non-directional van der Waals forces between molecule and surface, and covalent bonding of the acyl oxygen atoms with underlying Ag atoms, which is quantified by charge-transfer analysis. Furthermore, adsorption energy calculations showed that the molecular axis of flat-lying NTCDA is oriented preferably in parallel to the Ag rows. The molecule is subject to particular distortions from the planar gas phase structure with covalent bonding leading to downward bending of the acyl oxygen atoms and Pauli repulsion to upward bending of the carbon core. In parallel, strong buckling of the silver surface was identified. As found in previous studies, the lowest unoccupied molecular orbital (LUMO) of the molecule slips below the Fermi level and becomes partially populated upon adsorption. Excitation of totally symmetric vibrational modes then leads to substantial interfacial dynamical charge transfer, which is convincingly reproduced in the calculated IR spectra.