Characteristics of Lithium Ions and Superoxide Anions in EMI-TFSI and Dimethyl Sulfoxide.

To clarify the microscopic effects of solvents on the formation of the Li(+)-O2(­) process of a Li­O2 battery, we studied the kinetics and thermodynamics of these ions in dimethyl sulfoxide (DMSO) and 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide (EMI-TFSI) using classical molecular dynamics simulation. The force field for ions­solvents interactions was parametrized by force matching first-principles calculations. Despite the solvation energies of the ions are similar in both solvents, their mobility is much higher in DMSO. The free-energy profiles also confirm that the formation and decomposition rates of Li(+)-O2(­) pairs are greater in DMSO than in EMI-TFSI. Our atomistic simulations point out that the strong structuring of EMI-TFSI around the ions is responsible for these differences, and it explains why the LiO2 clusters formed in DMSO during the battery discharge are larger than those in EMI-TFSI. Understanding the origin of such properties is crucial to aid the optimization of electrolytes for Li­O2 batteries.

Efficient parametrization of complex molecule-surface force fields.

We present an efficient scheme for parametrizing complex molecule-surface force fields from ab initio data. The cost of producing a sufficient fitting library is mitigated using a 2D periodic embedded slab model made possible by the quantum mechanics/molecular mechanics scheme in CP2K. These results were then used in conjunction with genetic algorithm (GA) methods to optimize the large parameter sets needed to describe such systems. The derived potentials are able to well reproduce adsorption geometries and adsorption energies calculated using density functional theory. Finally, we discuss the challenges in creating a sufficient fitting library, determining whether or not the GA optimization has completed, and the transferability of such force fields to similar molecules.

Structural stability and polarisation of ionic liquid films on silica surfaces.

We used molecular dynamics simulations to investigate the effect of disorder of the hydroxylated amorphous silica surface on the structure of 8 nm IL films formed from two ionic liquids featuring the same cation 1-butyl-3-methyl-imidazolium or [BMIM], paired with bis(trifluoromethanesulphonyl)amide [NTF2] and tetrafluoroborate [BF4] anions. Several silica surfaces were modelled to estimate the effect of their atomic-scale configuration on the solid-liquid interface and the results are compared to those simulated on the crystalline cristobalite surface. Using strongly polar surfaces, we could also evaluate the response of the ILs to the electric field externally controlled or generated by charged defects in the silica film. We found that the structure of the liquids becomes weaker away from the interface and more susceptible to electric field. Our simulations show that [BMIM][BF4] has a large intrinsic dipole originating at the interface, resilient to external fields, while the polarisation of [BMIM][NTF2] can be more easily controlled.

Energy loss triggered by atomic-scale lateral force.

We perform bimodal atomic force microscopy measurements on a Br-doped NaCl (001) surface to investigate the mechanisms behind frequency shift and energy dissipation contrasts. The peculiar pattern of the dissipated energy in the torsional channel, related to frictional processes, is increased at the positions of Br impurities, otherwise indistinguishable from Cl ions in the other measured channels. Our simulations reveal how the energy dissipates by the rearrangement of the tip apex and how the process is ultimately governed by lateral forces. Even the slightest change in lateral forces, induced by the presence of a Br impurity, is enough to trigger the apex reconstruction more often, thus increasing the dissipation contrast; the predicted dissipation pattern and magnitude are in good quantitative agreement with the measurements.

Computed Three-Dimensional Atomic Force Microscopy Images of Biopolymers Using the Jarzynski Equality.

Three-dimensional atomic force microscopy (3D-AFM) has resolved three-dimensional distributions of solvent molecules at solid-liquid interfaces at the subnanometer scale. This method is now being extended to the imaging of biopolymer assemblies such as chromosomes or proteins in cells, with the expectation of being able to resolve their three-dimensional structures. Here, we have developed a computational method to simulate 3D-AFM images of biopolymers by using the Jarzynski equality. It is found that some parts of the fiber structure of biopolymers are indeed resolved in the 3D-AFM image. The dependency of 3D-AFM images on the vertical scanning velocity is investigated, and optimum scanning velocities are found. It is also clarified that forces in nonequilibrium processes are measured in 3D-AFM measurements when the dynamics of polymers are slower than the scanning of the probe.

Automated structure discovery in atomic force microscopy.

Atomic force microscopy (AFM) with molecule-functionalized tips has emerged as the primary experimental technique for probing the atomic structure of organic molecules on surfaces. Most experiments have been limited to nearly planar aromatic molecules due to difficulties with interpretation of highly distorted AFM images originating from nonplanar molecules. Here, we develop a deep learning infrastructure that matches a set of AFM images with a unique descriptor characterizing the molecular configuration, allowing us to predict the molecular structure directly. We apply this methodology to resolve several distinct adsorption configurations of 1S-camphor on Cu(111) based on low-temperature AFM measurements. This approach will open the door to applying high-resolution AFM to a large variety of systems, for which routine atomic and chemical structural resolution on the level of individual objects/molecules would be a major breakthrough.

Micrometre-long covalent organic fibres by photoinitiated chain-growth radical polymerization on an alkali-halide surface.

On-surface polymerization is a promising technique to prepare organic functional nanomaterials that are challenging to synthesize in solution, but it is typically used on metal substrates, which play a catalytic role. Previous examples on insulating surfaces have involved intermediate self-assembled structures, which face high barriers to diffusion, or annealing to higher temperatures, which generally causes rapid dewetting and desorption of the monomers. Here we report the photoinitiated radical polymerization, initiated from a two-dimensional gas phase, of a dimaleimide monomer on an insulating KCl surface. Polymer fibres up to 1 µm long are formed through chain-like rather than step-like growth. Interactions between potassium cations and the dimaleimide's oxygen atoms facilitate the propagation of the polymer fibres along a preferred axis of the substrate over long distances. Density functional theory calculations, non-contact atomic force microscopy imaging and manipulations at room temperature were used to explore the initiation and propagation processes, as well as the structure and stability of the resulting one-dimensional polymer fibres.

Self-Assembly Strategy for Fabricating Connected Graphene Nanoribbons.

We use self-assembly to fabricate and to connect precise graphene nanoribbons end to end. Combining scanning tunneling microscopy, Raman spectroscopy, and density functional theory, we characterize the chemical and electronic aspects of the interconnections between ribbons. We demonstrate how the substrate effects of our self-assembly can be exploited to fabricate graphene structures connected to desired electrodes.

Bottom-up graphene-nanoribbon fabrication reveals chiral edges and enantioselectivity.

We produce precise chiral-edge graphene nanoribbons on Cu{111} using self-assembly and surface-directed chemical reactions. We show that, using specific properties of the substrate, we can change the edge conformation of the nanoribbons, segregate their adsorption chiralities, and restrict their growth directions at low surface coverage. By elucidating the molecular-assembly mechanism, we demonstrate that our method constitutes an alternative bottom-up strategy toward synthesizing defect-free zigzag-edge graphene nanoribbons.

Using metallic noncontact atomic force microscope tips for imaging insulators and polar molecules: tip characterization and imaging mechanisms.

We demonstrate that using metallic tips for noncontact atomic force microscopy (NC-AFM) imaging at relatively large (>0.5 nm) tip-surface separations provides a reliable method for studying molecules on insulating surfaces with chemical resolution and greatly reduces the complexity of interpreting experimental data. The experimental NC-AFM imaging and theoretical simulations were carried out for the NiO(001) surface as well as adsorbed CO and Co-Salen molecules using Cr-coated Si tips. The experimental results and density functional theory calculations confirm that metallic tips possess a permanent electric dipole moment with its positive end oriented toward the sample. By analyzing the experimental data, we could directly determine the dipole moment of the Cr-coated tip. A model representing the metallic tip as a point dipole is described and shown to produce NC-AFM images of individual CO molecules adsorbed onto NiO(001) in good quantitative agreement with experimental results. Finally, we discuss methods for characterizing the structure of metal-coated tips and the application of these tips to imaging dipoles of large adsorbed molecules.