A Workflow for Identifying Viable Crystal Structures with Partially Occupied Sites Applied to the Solid Electrolyte Cubic Li7La3Zr2O12.

To date, experimental and theoretical works have been unable to uncover the ground-state configuration of the solid electrolyte cubic Li7La3Zr2O12 (c-LLZO). Computational studies rely on an initial low-energy structure as a reference point. Here, we present a methodology for identifying energetically favorable configurations of c-LLZO for a crystallographically predicted structure. We begin by eliminating structures that involve overlapping Li atoms based on nearest neighbor counts. We further reduce the configuration space by eliminating symmetry images from all remaining structures. Then, we perform a machine learning-based energetic ordering of all remaining structures. By considering the geometrical constraints that emerge from this methodology, we determine that a large portion of previously reported structures may not be feasible or stable. The method developed here could be extended to other ion conductors. We provide a database containing all of the generated structures with the aim of improving accuracy and reproducibility in future c-LLZO research.

Kinetically Corrected Monte Carlo-Molecular Dynamics Simulations of Solid Electrolyte Interphase Growth.

We present a kinetic approach to the Monte Carlo-molecular dynamics (MC-MD) method for simulating reactive liquids using nonreactive force fields. A graphical reaction representation allows definition of reactions of arbitrary complexity, including their local solvation environment. Reaction probabilities and molecular dynamics (MD) simulation times are derived from ab initio calculations. Detailed validation is followed by studying the development of the solid electrolyte interphase (SEI) in lithium-ion batteries. We reproduce the experimentally observed two-layered structure on graphite, with an inorganic layer close to the anode and an outer organic layer. This structure develops via a near-shore aggregation mechanism.

The simplest supramolecular helix.

Diethylamine is the smallest and simplest molecule that features a supramolecular helix as its lowest energy aggregate. Structural studies and large scale sampling simulations show that the helical arrangement is more stable than cyclic structures, which are the dominant species for other small hydrogen bonding molecules.

The solid state structures of the high and low temperature phases of dimethylcadmium.

The solid state structure of dimethylcadmium, a classic organometallic compound with a long history, has remained elusive for almost a century. X-ray crystallography and density functional theory reveal similar phase behaviour as in dimethylzinc. The high temperature tetragonal phase, α-Me2Cd, exhibits two-dimensional disorder, while the low temperature monoclinic phase, ß-Me2Cd, is ordered. Both phases contain linearly coordinated cadmium atoms. While the methyl groups are staggered in the α-phase, they are eclipsed in the ß-phase.

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.

Versatile bottom-up construction of diverse macromolecules on a surface observed by scanning tunneling microscopy.

The heterocoupling of organic building blocks to give complex multicomponent macromolecules directly at a surface holds the key to creating advanced molecular devices. While "on-surface" synthesis with prefunctionalized molecules has recently led to specific one- and two- component products, a central challenge is to discover universal connection strategies that are applicable to a wide range of molecules. Here, we show that direct activation of C-H bonds intrinsic to π-functional molecules is a highly generic route for connecting different building blocks on a copper surface. Scanning tunneling microscopy (STM) reveals that covalent π-functional macromolecular heterostructures, displaying diverse compositions, structures and topologies, are created with ease from seven distinct building blocks (including porphyrins, pentacene and perylene). By exploiting differences in C-H bond reactivity in the deposition and heating protocols we also demonstrate controlled synthesis of specific products, such as block copolymers. Further, the symmetry and geometry of the molecules and the surface also play a critical role in determining the outcome of the covalent bond forming reactions. Our "pick-mix-and-link" strategy opens up the capability to generate libraries of multivariate macromolecules directly at a surface, which in conjunction with nanoscale probing techniques could accelerate the discovery of functional interfaces.

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.

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.

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.

Thermally and vibrationally induced tautomerization of single porphycene molecules on a Cu(110) surface.

We report the direct observation of intramolecular hydrogen atom transfer reactions (tautomerization) within a single porphycene molecule on a Cu(110) surface by scanning tunneling microscopy. It is found that the tautomerization can be induced via inelastic electron tunneling at 5 K. By measuring the bias-dependent tautomerization rate of isotope-substituted molecules, we can assign the scanning tunneling microscopy-induced tautomerization to the excitation of specific molecular vibrations. Furthermore, these vibrations appear as characteristic features in the dI/dV spectra measured over individual molecules. The vibrational modes that are associated with the tautomerization are identified by density functional theory calculations. At higher temperatures above ∼75 K, tautomerization is induced thermally and an activation barrier of about 168 meV is determined from an Arrhenius plot.

Structure and stability of weakly chemisorbed ethene adsorbed on low-index Cu surfaces: performance of density functionals with van der Waals interactions.

We have investigated the performance of popular density functionals that include van der Waals interactions for the experimentally well-characterized problem of ethene (C(2)H(4)) adsorbed on the low-index surfaces of copper. This set of functionals does not only include three van der Waals density functionals-vdwDF-PBE, vdwDF-revPBE and optB86b-vdwDF-and two dispersion-corrected functionals-Grimme and TS-but also local and semi-local functionals such as LDA and PBE. The adsorption system of ethene on copper was chosen because it is a weakly chemisorbed system for which the vdW interactions are expected to give a significant contribution to the adsorption energy. Overall the density functionals that include vdW interactions increased substantially the adsorption energies compared to the PBE density functional but predicted the same adsorption sites and very similar C-C bonding distances except for two of the van der Waals functionals. The top adsorption site was predicted almost exclusively for all functionals on the (110), (100) and (111) surfaces, which is in agreement with experiment for the (110) surface but not for the (100) surface. On the (100) surface, all functionals except two van der Waals density functionals singled out the observed cross-hollow site from the calculated C-C bonding distances and adsorption heights. On the top sites on the (110) surface and the cross-hollow site on the Cu(100) surface, the ethene molecule was found to form a weak chemisorption bond. On the (111) surface, all functionals gave a C-C bonding distance and an adsorption height more typical for physisorption, in agreement with experiments.

Melting of hydrogen bonds in uracil derivatives probed by infrared spectroscopy and ab initio molecular dynamics.

The thermal response of hydrogen bonds is a crucial aspect in the self-assembly of molecular nanostructures. To gain a detailed understanding of their response, we investigated infrared spectra of monomers and hydrogen-bonded dimers of two uracil-derivative molecules, supported by density functional theory calculations. Matrix isolation spectra of monomers, temperature dependence in the solid state, and ab initio molecular dynamics calculations give a comprehensive picture about the dimer structure and dynamics of such systems as well as a proper assignment of hydrogen-bond affected bands. The evolution of the hydrogen bond melting is followed by calculating the C═O···H-N distance distributions at different temperatures. The result of this calculation yields excellent agreement with the H-bond melting temperature observed by experiment.

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.

High-resolution molecular orbital imaging using a p-wave STM tip.

Individual pentacene and naphthalocyanine molecules adsorbed on a bilayer of NaCl grown on Cu(111) were investigated by means of scanning tunneling microscopy using CO-functionalized tips. The images of the frontier molecular orbitals show an increased lateral resolution compared with those of the bare tip and reflect the modulus squared of the lateral gradient of the wave functions. The contrast is explained by tunneling through the p-wave orbitals of the CO molecule. Comparison with calculations using a Tersoff-Hamann approach, including s- and p-wave tip states, demonstrates the significant contribution of p-wave tip states.

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.

Clean coupling of unfunctionalized porphyrins at surfaces to give highly oriented organometallic oligomers.

The direct coupling of complex, functional organic molecules at a surface is one of the outstanding challenges in the road map to future molecular devices. Equally demanding is to meet this challenge without recourse to additional functionalization of the molecular building blocks and via clean surface reactions that leave no surface contamination. Here, we demonstrate the directional coupling of unfunctionalized porphyrin molecules--large aromatic multifunctional building blocks--on a single crystal copper surface, which generates highly oriented one-dimensional organometallic macromolecular nanostructures (wires) in a reaction which generates gaseous hydrogen as the only byproduct. In situ scanning tunneling microscopy and temperature programmed desorption, supported by theoretical modeling, reveal that the process is driven by C-H bond scission and the incorporation of copper atoms in between the organic components to form a very stable organocopper oligomer comprising organometallic edge-to-edge porphyrin-Cu-porphyrin connections on the surface that are unprecedented in solution chemistry. The hydrogen generated during the reaction leaves the surface and, therefore, produces no surface contamination. A remarkable feature of the wires is their stability at high temperatures (up to 670 K) and their preference for 1D growth along a prescribed crystallographic direction of the surface. The on-surface formation of directional organometallic wires that link highly functional porphyrin cores via direct C-Cu-C bonds in a single-step synthesis is a new development in surface-based molecular systems and provides a versatile approach to create functional organic nanostructures at surfaces.

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.

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.

Two-step mechanism for low-temperature oxidation of vacancies in graphene.

We study the oxidation of vacancies in graphene by ab initio atomistic thermodynamics to identify the dominant reaction mechanisms. Our calculations show that the low-temperature oxidation occurs via a two-step process: Vacancies are initially saturated by stable O groups, such as ether (C-O-C) and carbonyl (C=O). The etching is activated by a second step of additional O2 adsorption at the ether groups, forming larger O groups, such as lactone (C-O-C=O) and anhydride (O=C-O-C=O), that may desorb as CO2 just above room temperature. Our studies show that the partial pressure of oxygen is an important external parameter that affects the mechanisms of oxidation and that allows us to control the extent of etching.