Recreation of the periodic table with an unsupervised machine learning algorithm.

In 1869, the first draft of the periodic table was published by Russian chemist Dmitri Mendeleev. In terms of data science, his achievement can be viewed as a successful example of feature embedding based on human cognition: chemical properties of all known elements at that time were compressed onto the two-dimensional grid system for a tabular display. In this study, we seek to answer the question of whether machine learning can reproduce or recreate the periodic table by using observed physicochemical properties of the elements. To achieve this goal, we developed a periodic table generator (PTG). The PTG is an unsupervised machine learning algorithm based on the generative topographic mapping, which can automate the translation of high-dimensional data into a tabular form with varying layouts on-demand. The PTG autonomously produced various arrangements of chemical symbols, which organized a two-dimensional array such as Mendeleev's periodic table or three-dimensional spiral table according to the underlying periodicity in the given data. We further showed what the PTG learned from the element data and how the element features, such as melting point and electronegativity, are compressed to the lower-dimensional latent spaces.

Crystal Growth, Structural Analysis, and Pressure-Induced Superconductivity in a AgIn5Se8 Single Crystal Explored by a Data-Driven Approach.

A high-throughput first-principles calculation-assisted data-driven approach based on an inorganic materials database named AtomWork was performed to explore new superconducting materials. Specific band structures of a small band gap and flat band at band edges were used in a screening procedure. Among the candidates studied, we focused on AgIn5Se8, which shows a high density of state at the Fermi level. Single crystals of AgIn5Se8 were successfully obtained via a melt and slow cooling method. The valence states in AgIn5Se8 were estimated to be Ag1+, In3+, and Se2- using X-ray photoelectron spectroscopy. An electrical transport property of resistance was measured under high pressure using an electrodes-inserted diamond anvil cell. The sample exhibited an insulator-to-metal transition with a drastic decrease of the resistance by increasing the pressure up to 24.8 GPa. A possibility of a pressure-driven phase transition below this pressure was indicated by an enthalpy calculation. At a higher pressure region of 52.5 GPa, a pressure-induced superconducting transition was observed at 3.4 K. The maximum transition temperature was increased up to 3.7 K under the pressure of 74.0 GPa.

Computational study of positron annihilation parameters for cation mono-vacancies and vacancy complexes in nitride semiconductor alloys.

We calculate positron annihilation parameters, namely the S and W parameters from the Doppler broadening spectroscopy and the positron lifetime [Formula: see text], for defect-free states as well as cation mono-vacancies and vacancy complexes in nitride semiconductor alloys Al0.5Ga0.5N, In0.5Ga0.5N and Al0.5In0.5N. The obtained distributions of these parameters differ from compound to compound. Especially, the S-W relation for In0.5Ga0.5N is very different from that for Al0.5Ga0.5N. For the cation mono-vacancies, introducing local structural parameters, their correlations with S, W and [Formula: see text] are investigated. The S and [Formula: see text] variations are well described with the size distributions of the vacancies while the W variation is related to the presence of localized d electrons. For the vacancy complexes as well as the cation mono-vacancies, multiple-linear-regression models to describe S, W and [Formula: see text] are successfully constructed using the local structural parameters as descriptors. The S-W and S-[Formula: see text] relations are also compared with those for AlN, GaN and InN.

Data-driven exploration of new pressure-induced superconductivity in PbBi2Te4.

Candidate compounds for new thermoelectric and superconducting materials, which have narrow band gap and flat bands near band edges, were exhaustively searched by the high-throughput first-principles calculation from an inorganic materials database named AtomWork. We focused on PbBi2Te4 which has the similar electronic band structure and the same crystal structure with those of a pressure-induced superconductor SnBi2Se4 explored by the same data-driven approach. The PbBi2Te4 was successfully synthesized as single crystals using a melt and slow cooling method. The core level X-ray photoelectron spectroscopy analysis revealed Pb2+, Bi3+ and Te2- valence states in PbBi2Te4. The thermoelectric properties of the PbBi2Te4 sample were measured at ambient pressure and the electrical resistance was also evaluated under high pressure using a diamond anvil cell with boron-doped diamond electrodes. The resistance decreased with increasing of the pressure, and pressure-induced superconducting transitions were discovered at 2.5 K under 10 GPa. The maximum superconducting transition temperature increased up to 8.4 K at 21.7 GPa. The data-driven approach shows promising power to accelerate the discovery of new thermoelectric and superconducting materials.

Machine learning reveals orbital interaction in materials.

We propose a novel representation of materials named an 'orbital-field matrix (OFM)', which is based on the distribution of valence shell electrons. We demonstrate that this new representation can be highly useful in mining material data. Experimental investigation shows that the formation energies of crystalline materials, atomization energies of molecular materials, and local magnetic moments of the constituent atoms in bimetal alloys of lanthanide metal and transition-metal can be predicted with high accuracy using the OFM. Knowledge regarding the role of the coordination numbers of the transition-metal and lanthanide elements in determining the local magnetic moments of the transition-metal sites can be acquired directly from decision tree regression analyses using the OFM.

Novel mixture model for the representation of potential energy surfaces.

We demonstrate that knowledge of chemical physics on a materials system can be automatically extracted from first-principles calculations using a data mining technique; this information can then be utilized to construct a simple empirical atomic potential model. By using unsupervised learning of the generative Gaussian mixture model, physically meaningful patterns of atomic local chemical environments can be detected automatically. Based on the obtained information regarding these atomic patterns, we propose a chemical-structure-dependent linear mixture model for estimating the atomic potential energy. Our experiments show that the proposed mixture model significantly improves the accuracy of the prediction of the potential energy surface for complex systems that possess a large diversity in their local structures.

Active sites and mechanisms for oxygen reduction reaction on nitrogen-doped carbon alloy catalysts: Stone-Wales defect and curvature effect.

Carbon alloy catalysts (CACs) are promising oxygen reduction reaction (ORR) catalysts to substitute platinum. However, despite extensive studies on CACs, the reaction sites and mechanisms for ORR are still in controversy. Herein, we present rather general consideration on possible ORR mechanisms for various structures in nitrogen doped CACs based on the first-principles calculations. Our study indicates that only a particular structure of a nitrogen pair doped Stone-Wales defect provides a good active site. The ORR activity of this structure can be tuned by the curvature around the active site, which makes its limiting potential approaching the maximum limiting potential (0.80 V) in the volcano plot for the ORR activity of CACs. The calculated results can be compared with the recent experimental ones of the half-wave potential for CAC systems that range from 0.60 to 0.80 V in the reversible-hydrogen-electrode (RHE) scale.

Theoretical characterization of X-ray absorption, emission, and photoelectron spectra of nitrogen doped along graphene edges.

K-edge X-ray absorption (XAS), emission (XES), and photoelectron (XPS) spectra of nitrogen doped along graphene edges are systematically investigated by using first-principles methods. In this study we considered pyridinium-like, pyridine-like, cyanide-like, and amine-like nitrogens at armchair and zigzag edges and pyrrole-like nitrogen at armchair edge as well as graphite-like nitrogen at graphene interior site. Our results indicate that nitrogen configuration and its location (armchair or zigzag edge) in nitrogen-doped graphene can be identified via the spectral analysis. Furthermore, some controversial spectral features observed in experiment for N-doped graphene-like materials are unambiguously assigned. The present analysis gives an explanation to the reason why the peak assignment is usually made differently between XPS and XAS.

Charge-transport in tin-iodide perovskite CH3NH3SnI3: origin of high conductivity.

The structural and electrical properties of a metal-halide cubic perovskite, CH(3)NH(3)SnI(3), have been examined. The band structure, obtained using first-principles calculation, reveals a well-defined band gap at the Fermi level. However, the temperature dependence of the single-crystal electrical conductivity shows metallic behavior down to low temperatures. The temperature dependence of the thermoelectric power is also metallic over the whole temperature range, and the large positive value indicates that charge transport occurs with a low concentration of hole carriers. The metallic properties of this as-grown crystal are thus suggested to result from spontaneous hole-doping in the crystallization process, rather than the semi-metal electronic structure. The present study shows that artificial hole doping indeed enhances the conductivity.

Hydration properties of magnesium and calcium ions from constrained first principles molecular dynamics.

We studied the solvation structures of the divalent metal cations Mg(2+) and Ca(2+) in ambient water by applying a Car-Parrinello-based constrained molecular dynamics method. By employing the metal-water oxygen coordination number as a reaction coordinate, we could identify distinct aqua complexes characterized by structural variations of the first coordination shell. In particular, our estimated free-energy profile clearly shows that the global minimum for Mg(2+) is represented by a rather stable sixfold coordination in the octahedral arrangement, in agreement with experiments. Conversely, for Ca(2+) the free-energy curve shows several shallow local minima, suggesting that the hydration structure of Ca(2+) is highly variable. Implications for water exchange reactions are also discussed.

Hydration of alkali ions from first principles molecular dynamics revisited.

Structural and dynamical properties of the hydration of Li(+), Na(+), and K(+) in liquid water at ambient conditions were studied by first principles molecular dynamics. Our simulations successfully captured the different hydration behavior shown by the three alkali ions as observed in experiments. The present analyses of the dependence of the self-diffusion coefficient and rotational correlation time of water on the ion concentration suggest that Li(+) (K(+)) is certainly categorized as a structure maker (breaker), whereas Na(+) acts as a weak structure breaker. An analysis of the relevant electronic structures, based on maximally localized Wannier functions, revealed that the dipole moment of H(2)O molecules in the first solvation shell of Na(+) and K(+) decreases by about 0.1 D compared to that in the bulk, due to a contraction of the oxygen lone pair orbital pointing toward the metal ion.

Hsc70 ATPase: an insight into water dissociation and joint catalytic role of K+ and Mg2+ metal cations in the hydrolysis reaction.

Hybrid quantum mechanics/molecular mechanics simulations, coupled to the recently introduced metadynamics method, performed on the adenosine triphosphate (ATP) of the bovine Hsc70 ATPase protein, show which specific water molecule of the solvation shell of the Mg2+ metal cation acts as a trigger in the initial phase of the ATP hydrolysis reaction in ATP synthase. Furthermore, we provide a detailed picture of the reaction mechanism, not accessible to experimental probes, that allows us to address two important issues not yet unraveled: (i) the pathway followed by a proton and a hydroxyl anion, produced upon dissociation of a putative catalytic H2O molecule, that is crucial in the selection of the reaction channel leading to the hydrolysis; (ii) the unique and cooperative role of K+ and Mg2+ metal ions in the reaction, acting as co-catalysts and promoting the release of the inorganic phosphate via an exchange of the OH- hydroxyl anion between their respective solvation shells. This is deeply different from the proton wire mechanism evidenced, for instance, in actin and lowers significantly the free energy barrier of the reaction.

Double-Metal-Ion/Single-Metal-Ion Mechanisms of the Cleavage Reaction of Ribozymes: First-Principles Molecular Dynamics Simulations of a Fully Hydrated Model System.

The role of metal cations (Mg(2+)) in the cleavage reaction of fully hydrated RNA enzymes is investigated via Car-Parrinello calculations. We find that the action of two metal catalysts is the most efficient way to promote, on one hand, the proton abstraction from O(2)(')-H that triggers the nucleophilic attack and, on the other hand, the weakening and subsequent cleavage of the P-O(5)(') bond. The elimination of one of the two metal cations is shown to lead to an increase in the activation energy. Furthermore, we also find that an OH(-) included in the coordination shell of the Mg(2+) close to O(2)(') promotes the initial proton abstraction and prevents its transfer to the ribozyme in both single- and double-metal-ion pathways, consistently with the experiment. This suggests that in real ribozyme systems, the double-metal-ion reaction mechanism in the presence of an OH(-) anion is favored with respect to single-metal-ion mechanisms.

Hydrogen bond driven chemical reactions: Beckmann rearrangement of cyclohexanone oxime into epsilon-caprolactam in supercritical water.

Recent experiments have shown that supercritical water (SCW) has the ability to accelerate and make selective synthetic organic reactions, thus replacing the common but environmentally harmful acid and basic catalysts. In an attempt to understand the intimate mechanism behind this observation, we analyze, via first-principles molecular dynamics, the Beckmann rearrangement of cyclohexanone oxime into epsilon-caprolactam in supercritical water, for which accurate experimental evidence has been reported. Differences in the wetting of the hydrophilic parts of the solute, enhanced by SCW, and the disrupted hydrogen bond network are shown to be crucial in triggering the reaction and in making it selective. Furthermore, the enhanced concentrations of H(+) in SCW play an important role in starting the reaction.

The anomalous Hall effect and magnetic monopoles in momentum space.

Efforts to find the magnetic monopole in real space have been made in cosmic rays and in particle accelerators, but there has not yet been any firm evidence for its existence because of its very heavy mass, approximately 10(16) giga-electron volts. We show that the magnetic monopole can appear in the crystal momentum space of solids in the accessible low-energy region (approximately 0.1 to 1 electron volts) in the context of the anomalous Hall effect. We report experimental results together with first-principles calculations on the ferromagnetic crystal SrRuO3 that provide evidence for the magnetic monopole in the crystal momentum space.

First-principles molecular-dynamics simulations of a hydrated electron in normal and supercritical water.

A first principles study of a hydrated electron in water at ordinary and supercritical conditions is presented. In the first case, the electron cleaves a cavity in the hydrogen bond network in which six H2O molecules form the solvation shell. The electron distribution assumes an ellipsoidal shape, and the agreement of the computed and the experimental optical absorption seems to support this picture. At supercritical conditions, instead, the H-bond network is not continuous and allows us to predict that the electron localizes in preexisting cavities in a more isotropic way. Four water molecules form the solvation shell but the localization time shortens significantly.

Catalytic role of metal ion in the selection of competing reaction paths: a first principles molecular dynamics study of the enzymatic reaction in ribozyme.

By using finite temperature first principles molecular dynamics, the mechanism of the enzymatic reaction of ribozyme was investigated for both the anionic and the radical charge states of the modeled RNA fragment. In the case of the anionic system, a pseudorotation and the subsequent 3' --> 2' migration occur in a vacuum, rather than the self-cleavage of the phosphodiester. On the other hand, when either a divalent metal ion (Mg(2+)) catalyst or the continuous hydrogen bond network of the solvent is present, the reaction path of the anionic species changes dramatically, going toward the transesterification channel. In a radical system, the transesterification can occur without a metal catalyst, as a consequence of the displacement of a hole (empty electronic state) along the reaction path. Thus, the present analysis suggests that a metal ion might be essential not only in lowering the activation barrier but also in selecting the reaction path among those corresponding to possible different charge states of the intermediate structure in vivo. Furthermore, simulation of the anionic species in solution shows that, in the absence of a metal catalyst, water molecules cooperate with the proton transfer via a proton wire mechanism and the hydrogen bond network plays a crucial role in preventing pseudorotations. On the other hand, when a metal cation is present in the vicinity of the site where the nucleophilic attack occurs, the hydrogen bond network is interrupted and detachment of the proton, enhanced by the catalyst, does not give rise to any proton-transfer process.