Topological Data analysis of Ion Migration Mechanism.

Topological data analysis based on persistent homology has been applied to the molecular dynamics simulation for the fast ion-conducting phase (α-phase) of AgI to show its effectiveness on the ion migration mechanism analysis. Time-averaged persistence diagrams of α-AgI, which quantitatively record the shape and size of the ring structures in the given atomic configurations, clearly showed the emergence of the four-membered rings formed by two Ag and two I ions at high temperatures. They were identified as common structures during the Ag ion migration. The averaged potential energy change due to the deformation of the four-membered ring during Ag migration agrees well with the activation energy calculated from the conductivity Arrhenius plot. The concerted motion of two Ag ions via the four-membered ring was also successfully extracted from molecular dynamics simulations by our approach, providing new insight into the specific mechanism of the concerted motion.

Complementary Design for Pairing between Two Types of Nanoparticles Mediated by a Bispecific Antibody: Bottom-Up Formation of Porous Materials from Nanoparticles.

Recent advances in biotechnology have enabled the generation of antibodies with high affinity for the surfaces of specific inorganic materials. Herein, we report the synthesis of functional materials from multiple nanomaterials by using a small bispecific antibody recombinantly constructed from gold-binding and ZnO-binding antibody fragments. The bispecific antibody-mediated spontaneous linkage of gold and ZnO nanoparticles forms a binary gold-ZnO nanoparticle composite membrane. The relatively low melting point of the gold nanoparticles and the solubility of ZnO in dilute acidic solution then allowed for the bottom-up synthesis of a nanoporous gold membrane by means of a low-energy, low-environmental-load protocol. The nanoporous gold membrane showed high catalytic activity for the reduction of p-nitrophenol to p-aminophenol by sodium borohydride. Here, we show the potential utility of nanoparticle pairing mediated by bispecific antibodies for the bottom-up construction of nanostructured materials from multiple nanomaterials.

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.

Imaging the evolution of d states at a strontium titanate surface.

Oxide electronics is a promising alternative to the conventional silicon-based semiconductor technology, owing to the rich functionalities of oxide thin films and heterostructures. In contrast to the silicon surface, however, the electronic structure of the SrTiO3 surface, the most important substrate for oxide thin films growth, is not yet completely understood. Here we report on the electronic states of a reconstructed (001) surface of SrTiO3 determined in real space, with scanning tunneling microscopy/spectroscopy and density functional theory calculations. We found a remarkable energy dependence of the spectroscopic image: Theoretical analysis reveals that symmetry breaking at the surface lifts the degeneracy in the t2g state (dxy, dyz, and dzx) of Ti 3d orbitals, whose anisotropic spatial distribution leads to a sharp transition in the spectroscopic image as a function of energy. The knowledge obtained here could be used to gain further insights into emergent phenomena at the surfaces and interfaces with SrTiO3.

Linear regression model for metal-organic frameworks with CO2 adsorption based on topological data analysis.

Metal-organic frameworks (MOFs), self-assembled porous materials synthesized from metal ions and organic ligands, are promising candidates for the direct capture of CO2 from the atmosphere. In this work, we developed a regression model to predict the optimal component of the MOF that governs the amount of CO2 adsorption per volume based on experimentally observed adsorption and structure data combined with MOF adsorption sites. The structural descriptors were generated by topological data analysis with persistence diagrams, an advanced mathematical method for quantifying the rings and cavities within the MOF. This enables us to analyze direct effects and significance of the geometric structure of the MOF on the efficiency of CO2 adsorption in a novel way. The proposed approach is proved to be highly correlated with experimental data and thus offers an effective screening tool for MOFs with optimized structures.

N-Phenyl-N-[(E)-2-(4,4,5,5-tetra-methyl-1,3,2-dioxaborolan-2-yl)ethen-yl]aniline.

The title compound, C20H24BNO2, has a polarized π-system due to significant resonance between the N-C(H)=C(H)-B and ionic N+=C(H)-C(H)=B- canonical forms. The dihedral angles between the NC2B plane (r.m.s. deviation 0.0223 Å) and the C3N (r.m.s. deviation 0.0025 Å) and BCO2 (r.m.s. deviation 0.0044 Å) planes are 2.51 (12) and 3.09 (19)°, respectively. This indicates the lone pair of the nitro-gen atom and a vacant p orbital of the boron atom are conjugated with the central C=C bond. In comparison with the carbazole analogue [Hatayama & Okuno (2012 ▸). Acta Cryst. E68, o84], the C-N and C-B bonds are shorter. The results are well explained by the increase in the contribution of the N+=C(H)-C(H)=B- canonical form in the title compound.

9-[(Z)-2-(4,4,5,5-Tetra-methyl-1,3,2-dioxaborolan-2-yl)ethen-yl]-9H-carbazole.

The title compound, C20H22BNO2, has a polarized π-system due to resonance between N-C(H)=C(H)-B and ionic N+=C(H)-C(H)=B- canonical structures. The dihedral angles between the ethenyl plane (r.m.s. deviation for C2H2 = 0.0333 Å) with the ethenyl-C(NC2-pyrrole) plane (r.m.s. deviation CNC2 0.0423 Å) and the ethenyl-C(BO2-1,3,2-dioxaborolane) plane (r.m.s. deviation BCO2 0.0082 Å) are 45.86 (8) and 37.47 (8)°, respectively, and are greater than those found for the previously reported E-isomer [Hatayama & Okuno (2012 ▸) Acta Cryst. E68, o84]. In comparison with the E-isomer, the reduced planarity of Z-isomer results in a decrease of the contribution of the N+=C(H)-C(H)=B- canonical structure.

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.

Regioselective cycloaddition reaction of alkene molecules with the asymmetric dimer on Si(100)c(4 x 2).

We investigated the adsorption states of 2-methylpropene and propene on Si(100)c(4 x 2) using low-temperature scanning tunneling microscopy. We have found that regioselective cycloaddition reactions (di-sigma bond formation) occur between the asymmetric alkene molecules and the asymmetric dimers on Si(100)c(4 x 2). First-principles calculations have elucidated that the regioselectivity is closely related to the structures of precursor species and these precursor species have carbocation-like features. Thus, we conclude that Markovnikov's rule is applicable for the cycloaddition of asymmetric alkene with the asymmetric dimer on Si(100)c(4 x 2).

Precursor mediated cycloaddition reaction of ethylene to the Si(100)c(4 x 2) surface.

We report the direct observation of a precursor state for the cycloaddition reaction (the di-sigma bond formation) of ethylene on Si(100)c(4 x 2) using high-resolution electron energy loss spectroscopy at low temperature, and the meta-stable precursor state is identified as a weakly bonded pi-complex type. The activation energy from the pi-complex precursor to the di-sigma bonded species is experimentally estimated to be 0.2 eV. First-principles calculations support the pi-complex precursor mediated cycloaddition reaction of ethylene on Si(100)c(4 x 2).