Felix Hanke

Ab initio molecular simulations with numeric atom-centered orbitals

We describe a complete set of algorithms for ab initio molecular simulations based on numerically tabulated atom-centered orbitals (NAOs) to capture a wide range of molecular and materials properties from quantum-mechanical first principles. The full algorithmic framework described here is embodied in the Fritz Haber Institute “ab initio molecular simulations” (FHI-aims) computer program package. Its comprehensive description should be relevant to any other first-principles implementation based on NAOs. The focus here is on density-functional theory (DFT) in the local and semilocal (generalized gradient) approximations, but an extension to hybrid functionals, Hartree–Fock theory, and MP2/GW electron self-energies for total energies and excited states is possible within the same underlying algorithms. An all-electron/full-potential treatment that is both computationally efficient and accurate is achieved for periodic and cluster geometries on equal footing, including relaxation and ab initio molecular dynamics. We demonstrate the construction of transferable, hierarchical basis sets, allowing the calculation to range from qualitative tight-binding like accuracy to meV-level total energy convergence with the basis set. Since all basis functions are strictly localized, the otherwise computationally dominant grid-based operations scale as O(N) with system size N. Together with a scalar-relativistic treatment, the basis sets provide access to all elements from light to heavy. Both low-communication parallelization of all real-space grid based algorithms and a ScaLapack-based, customized handling of the linear algebra for all matrix operations are possible, guaranteeing efficient scaling (CPU time and memory) up to massively parallel computer systems with thousands of CPUs.

Mechanisms of halogen-based covalent self-assembly on metal surfaces

We computationally study the reaction mechanisms of halogen-based covalent self-assembly, a major route for synthesizing molecular nanostructures and nanographenes on surfaces. Focusing on biphenyl as a small model system, we describe the dehalogenation, recombination, and diffusion processes. The kinetics of the different processes are also investigated, in particular how diffusion and coupling barriers affect recombination rates. Trends across the periodic table are derived from three commonly used close-packed (111) surfaces (Cu, Ag, and Au) and two halogens (Br and I). We show that the halogen atoms can poison the surface, thus hindering long-range ordering of the self-assembled structures. Finally, we present core-level shifts of the relevant carbon and halogen atoms, to provide reference data for reliably detecting self-assembly without the need for atomic-resolution scanning tunneling microscopy.

Controlling intramolecular hydrogen transfer in a porphycene molecule with single atoms or molecules located nearby

Although the local environment of a molecule can play an important role in its chemistry, rarely has it been examined experimentally at the level of individual molecules. Here we report the precise control of intramolecular hydrogen-transfer (tautomerization) reactions in single molecules using scanning tunnelling microscopy. By placing, with atomic precision, a copper adatom close to a porphycene molecule, we found that the tautomerization rates could be tuned up and down in a controlled fashion, surprisingly also at rather large separations. Furthermore, we extended our study to molecular assemblies in which even the arrangement of the pyrrolic hydrogen atoms in the neighbouring molecule influences the tautomerization reaction in a given porphycene, with positive and negative cooperativity effects. Our results highlight the importance of controlling the environment of molecules with atomic precision and demonstrate the potential to regulate processes that occur in a single molecule.

Zipping Up: Cooperativity Drives the Synthesis of Graphene Nanoribbons

We investigate the cooperative effects controlling the synthesis of a graphene nanoribbon on the Au(111) surface starting from an anthracene polymer using density functional calculations including van der Waals interactions. We focus on the high-temperature cyclodehydrogenation step of the reaction and find that the reaction proceeds by simultaneously transferring two H-atoms from the anthracene units to the Au surface, leaving behind a C-C bond in the process. This step is significantly more favorable than the three other potential reaction paths. Moreover, we find that successive dehydrogenations proceed from one end of the polyanthracene and propagate step-by-step through the polymer in a domino-like fashion.

Heat-to-Connect: Surface Commensurability Directs Organometallic One-Dimensional Self-Assembly

Recent experiments demonstrated the assembly of unfunctionalized porphyrin molecules into organometallic wires on the Cu(110) surface through the formation of stable C-Cu-C bonds involving Cu adatoms. The remarkable property of the observed structures is that they adopt a clear direction, despite the lack of functional ligands to direct the assembly. Here we use density functional theory calculations and scanning tunneling microscopy to clarify the mechanism for the highly one-dimensional assembly of the observed nanostructures. An energetic preference for the formation of C-Cu-C bonds is found in several lattice directions, but self-assembly critically relies on the commensurability of appropriate adsorption sites for the Cu atoms involved in the coupling. The experimentally observed structures arise from a geometric self-limitation of the assembly process, which proceeds in the energetically and geometrically most preferred direction. A further extension of the structure in the orthogonal dimension to form 2D assemblies is prevented by the lattice mismatch between the repeat lengths in the 001 and 110 directions of the underlying (110) lattice and the apparent rigidity of the molecules involved. However, the fusing of two parallel chains is geometrically allowed and leads to some of the energetically most favorable configurations. Finally, the role of van der Waals forces is investigated for the covalent couplings and chemisorbed interactions found in this system.

Towards Design Rules for Covalent Nanostructures on Metal Surfaces

The covalent molecular assembly on metal surfaces is explored, outlining the different types of applicable reactions. Density functional calculations for on-surface reactions are shown to yield valuable insights into specific reaction mechanisms and trends across the periodic table. Finally, it is shown how design rules could be derived for nanostructures on metal surfaces.

The Solid-State Structures of Dimethylzinc and Diethylzinc

The synthesis of dimethylzinc (Me2Zn) and diethylzinc (Et2Zn) by Frankland in the mid-nineteenth century marks a cornerstone in the history of chemistry.1 Not only were they among the first organometallic compounds, but studies on their chemical reactions and vapor densities led to the first clear exposition of valency theory.2 Since then both compounds have found widespread applications: They are important reagents in organic synthesis,3 for example in the enantioselective alkylation of carbonyls4 and imines5 and in cyclopropanation reactions.6 Their high vapor pressures have led to extensive uses in metalorganic chemical vapor deposition (MOCVD) for the preparation of wide band gap II–VI semiconducting films (e.g. ZnS, ZnSe, ZnTe),7 ZnO nanostructures, and as p-dopant precursors for III–V semiconductors (e.g. GaAs, InP, AlxGa1−xAs), which have numerous electronic and photonic applications.8

Sensitivity analysis and uncertainty calculation for dispersion corrected density functional theory

The precision of binding energies and distances computed with dispersion‐corrected density functional theory (DFT‐D) is investigated by propagation of uncertainties, yielding relative uncertainties of several percent. Sensitivity analysis is used to calculate the geometry‐dependent relative importance of each input parameter for the dispersion correction. While DFT‐Ds are exact at asymptotically large distances, their damping functions are shown to play a significant role in binding geometries. This is demonstrated in detail for the interlayer binding of graphite. The techniques presented allow practitioners to quickly compute error bars and to get an a posteriori estimate about the transferability of their results. They can also aid the development of future dispersion corrections.

Adatoms underneath Single Porphyrin Molecules on Au(111)

The adsorption of porphyrin derivatives on a Au(111) surface was studied by scanning tunneling microscopy and spectroscopy at low temperatures in combination with density functional theory calculations. Different molecular appearances were found and could be assigned to the presence of single gold adatoms bonded by a coordination bond underneath the molecular monolayer, causing a characteristic change of the electronic structure of the molecules. Moreover, this interpretation could be confirmed by manipulation experiments of individual molecules on and off a single gold atom. This study provides a detailed understanding of the role of metal adatoms in surface-molecule bonding and anchoring and of the appearance of single molecules, and it should prove relevant for the imaging of related molecule-metal systems.

Rigid Dimers Formed through Strong Interdigitated H‐Bonds Yield Compact 1D Supramolecular Helical Polymers

Hierarchical self-assembly of small abiotic molecular modules interacting through noncovalent forces is increasingly being used to generate functional structures and materials for electronic, catalytic, and biomedical applications. The greatest control over the geometry in H-bond supramolecular architectures, especially in H-bonded supramolecular polymers, can be achieved by using conformationally rigid molecular modules undergoing self-assembly through strong H-bonds. Their binding strength depends on the multiplicity of the H-bonds, the nature of donor/acceptor pairs and their secondary attractive/repulsive interactions. Here a functionalized molecular module is described, which is capable of self-associating through self-complementary H-bonding patterns comprising four strong and two medium-strength H-bonds to form dimers. The self-association of these phenylpyrimidine-based dimers through directional H-bonding between two lateral pyridin-2(1H)-one units of neighboring molecules allows the formation of highly compact 1D supramolecular polymers by self-assembly on graphite. A concentration-dependent study by scanning tunneling microscopy at the solid-liquid interface, corroborated by dispersion-corrected density functional studies, reveals the controlled generation of either linear supramolecular 2D arrays, or long helical supramolecular polymers with a high shape persistence.