Beyond metals: theoretical discovery of semiconducting MAX phases and their potential application in thermoelectrics.

MAX phase is a family of ceramic compounds, typically known for their metallic properties. However, we show here that some of them may be narrow bandgap semiconductors. Using a series of first-principles calculations, we have investigated the electronic structures of 861 dynamically stable MAX phases. Notably, Sc2SC, Y2SC, Y2SeC, Sc3AuC2, and Y3AuC2 have been identified as semiconductors with band gaps ranging from 0.2 to 0.5 eV. Furthermore, we have assessed the thermodynamic stability of these systems by generating ternary phase diagrams utilizing evolutionary algorithm techniques. Their dynamic stabilities are confirmed by phonon calculations. Additionally, we have explored the potential thermoelectric efficiencies of these materials by combining Boltzmann transport theory with first-principles calculations. The relaxation times are estimated using scattering theory. The zT coefficients for the aforementioned systems fall within the range of 0.5 to 2.5 at temperatures spanning from 300 to 700 K, indicating their suitability for high-temperature thermoelectric applications.

Non-adiabatic excited-state time-dependent GW molecular dynamics (TDGW) satisfying extended Koopmans' theorem: An accurate description of methane photolysis.

There is a longstanding difficulty that time-dependent density functional theory relying on adiabatic local density approximation is not applicable to the electron dynamics, for example, for an initially excited state, such as in photochemical reactions. To overcome this, we develop non-adiabatic excited-state time-dependent GW molecular dynamics (TDGW) on the basis of the extended quasiparticle theory. Replacing Kohn-Sham orbitals/energies with correlated, interacting quasiparticle orbitals/energies allows the full correspondence to the excited-state surfaces and corresponding total energies, with satisfying extended Koopmans' theorem. We demonstrate the power of TDGW using methane photolysis, CH4→CH3•+H, an important initiation reaction for combustion/pyrolysis and hydrogen production of methane. We successfully explore several possible pathways and show how this reaction dynamics is captured accurately through simultaneously time-tracing all quasiparticle levels. TDGW scales as O(NB3-4), where NB is the number of basis functions, which is distinctly advantageous to performing dynamics using configuration interaction and coupled cluster methods.

Extended quasiparticle approach to non-resonant and resonant X-ray emission spectroscopy.

The initial states of the secondary processes of X-ray emission spectroscopy (XES) and resonant inelastic X-ray scattering (RIXS) are highly excited eigenstates with a deep core hole after a X-ray photoelectron spectroscopy (XPS) process and a X-ray photoabsorption spectroscopy (XAS) process, respectively, so that the XES and RIXS calculation offers a good example of extended quasiparticle theory (EQPT) (K. Ohno, S. Ono and T. Isobe, J. Chem. Phys., 2017, 146, 084108) which is applicable to any initial exited eigenstate. We apply the standard one-shot GW + Bethe-Salpeter equation (BSE) approach in MBPT to this problem on the basis of EQPT and analyze XES and RIXS spectra for CH4, NH3, H2O, and CH3OH molecules. We also suggest a simpler approach only using the GW calculation without solving the BSE to compute the XES and RIXS energies, although it cannot give the spectral intensity. Moreover, according to extended Kohn-Sham theory (T. Nakashima, H. Raebiger and K. Ohno, Phys. Rev. B, 2021, 104, L201116), we give a justification and comment of applying the method relying on time-dependent density functional theory as well as the one-shot GW + BSE approach to this problem.

First principles calculations of surface dependent electronic structures: a study on ß-FeOOH and γ-FeOOH.

We report a theoretical study on iron oxyhydroxide (FeOOH). The FeOOH surface is expected to act as an efficient electrochemical catalyst for the oxygen evolution reaction (OER), because it is based on iron, an element of the fourth highest Clarke number. Experimentally, the OER activity of ß-FeOOH is known to be higher than that of γ-FeOOH. However, the details of the OER mechanism and the surface reactivities of the FeOOH polymorphs have not yet been fully understood. We performed first-principles calculations of bulk and surfaces of ß-FeOOH and γ-FeOOH using density functional theory, to investigate their electronic structures and catalytic activities. The calculations suggest that depending on the surface indices, several surfaces may be favored for catalytic activities.

Carbon Monoxide Hydrogenation on Ice Surfaces.

We have performed density functional calculations to investigate the carbon monoxide hydrogenation reaction (H+CO→HCO), which is important in interstellar clouds. We found that the activation energy of the reaction on amorphous ice is lower than that on crystalline ice. In the course of this study, we demonstrated that it is roughly possible to use the excitation energy of the reactant molecule (CO) in place of the activation energy. This relationship holds also for small water clusters at the CCSD level of calculation and the two-layer-level ONIOM (CCSD : X3LYP) calculation. Generally, since it is computationally demanding to estimate activation energies of chemical reactions in a circumstance of many water molecules, this relationship enables one to determine the activation energy of this reaction on ice surfaces from the knowledge of the excitation energy of CO only. Incorporating quantum-tunneling effects, we discuss the reaction rate on ice surfaces. Our estimate that the reaction rate on amorphous ice is almost twice as large as that on crystalline ice is qualitatively consistent with the experimental evidence reported by Hidaka et al. [Chem. Phys. Lett., 2008, 456, 36.].

First-principles study on the atomistic corrosion processes of iron.

The corrosion of iron presents an important scientific problem and a serious economic issue. It is also one of the most important subjects in materials science because it is basically an electrochemical process and closely related to other topics such as the electrocatalysis of the oxygen reduction reaction. So far, many studies have been conducted to address the corrosion of iron, a very complicated process that occurs when iron is exposed to oxygen and water. An important question is, at which site of the iron surface the corrosion starts and how it results in the final stage of the corrosion. In the present study, as an example of superficial defects, Fe dimers sticking out of Fe(100) surfaces are considered in order to understand the iron corrosion process from first-principles using density functional theory. We found that the Fe dimers spontaneously react with O2 and H2O to form Fe2(OH)4 + 4OH-. Here, it is interesting to note that the Fe dimer plays the role of a water splitting catalyst, because the space above it is always vacant and can accept oxygen molecules many times for reacting with the surrounding water molecules. Then, if the Fe2(OH)4 molecules are detached from the surface, they react with O2 to form Fe2O(OH)4 without an activation barrier, and, in turn, the Fe2O(OH)4 and H2O molecules react to form Fe2(OH)6 complexes with an activation energy of 0.653 eV. If these complexes further dissociate into Fe(OH)3 molecules, they react with each other to form Fe2O3·2H2O with an activation energy of 0.377 eV. This work may provide useful information on possible iron corrosion processes by water in the air.

A simple derivation of the exact quasiparticle theory and its extension to arbitrary initial excited eigenstates.

The quasiparticle (QP) energies, which are minus of the energies required by removing or produced by adding one electron from/to the system, corresponding to the photoemission or inverse photoemission (PE/IPE) spectra, are determined together with the QP wave functions, which are not orthonormal and even not linearly independent but somewhat similar to the normal spin orbitals in the theory of the configuration interaction, by self-consistently solving the QP equation coupled with the equation for the self-energy. The electron density, kinetic, and all interaction energies can be calculated using the QP wave functions. We prove in a simple way that the PE/IPE spectroscopy and therefore this QP theory can be applied to an arbitrary initial excited eigenstate. In this proof, we show that the energy-dependence of the self-energy is not an essential difficulty, and the QP picture holds exactly if there is no relaxation mechanism in the system. The validity of the present theory for some initial excited eigenstates is tested using the one-shot GW approximation for several atoms and molecules.

Momentum-dependent band spin splitting in semiconducting MnO2: a density functional calculation.

Recently, manganese-oxide compounds have attracted considerable attention, in particular, as candidate materials for photochemical water-splitting reactions. Here, we investigate electronic states of pristine manganese dioxides (MnO2) in different crystal phases using spin-polarized density functional theory (DFT) with Hubbard U correction. Geometrical structures and band dispersions of α-, ß-, δ-, and λ-MnO2 crystals with collinear magnetic [ferromagnetic (FM) and antiferromagnetic (AFM)] orders are discussed in detail. We reveal that penalty energies that arise by violating the Goodenough-Kanamori rule are important and the origin of the magnetic interactions of the MnO2 crystals is governed by the superexchange interactions of Mn-O-Mn groups. In addition, it is found that momentum-dependent band spin splitting occurs in the AFM α-, ß-, and δ-MnO2 crystals while no spin splitting occurs in the AFM λ-MnO2 crystal. Our results show that spin-split band dispersions stem from the different orientations of Mn-centred oxygen octahedra. Such interesting electronic states of the MnO2 crystals are unraveled by our discussion on the relationship between the effective (spin-dependent) single-electron potentials and the space-group symmetry operations that map up-spin Mn atoms onto down-spin Mn atoms. This work provides a basis to understand the relationship between the spin-dependent electronic states and the crystallography of manganese oxides. Another relationship to the recent experimental observations of the photochemical oxygen evolution of MnO2 crystals is also discussed.

A self-consistent GW approach to the van der Waals potential for a helium dimer.

van der Waals interaction between two helium (He) atoms is studied by calculating the total energy as a function of the He-He distance within the self-consistent GW approximation, which is expected to behave correctly in the long wavelength limit. In the Born-Oppenheimer (BO) approximation, the pair potential curve has its minimum value at 2.87 Å, which is somewhat larger than the local density approximation result, 2.40 Å, and is closer to previous quantum chemistry results. The expectation value for the interatomic distance, calculated by solving the Schrödinger equation for the two nuclei problem using the BO potential energy curve, is 30 Å, which is smaller but of the same order as previous experimental and theoretical results.

Ab initio molecular dynamics simulation study of successive hydrogenation reactions of carbon monoxide producing methanol.

Doing ab initio molecular dynamics simulations, we demonstrate a possibility of hydrogenation of carbon monoxide producing methanol step by step. At first, the hydrogen atom reacts with the carbon monoxide molecule at the excited state forming the formyl radical. Formaldehyde was formed after adding one more hydrogen atom to the system. Finally, absorption of two hydrogen atoms to formaldehyde produces methanol molecule. This study is performed by using the all-electron mixed basis approach based on the time dependent density functional theory within the adiabatic local density approximation for an electronic ground-state configuration and the one-shot GW approximation for an electronic excited state configuration.

Relationship between cap structure and energy gap in capped carbon nanotubes.

Revealing a universal relation between geometrical structures and electronic properties of capped carbon nanotubes (CNTs) is one of the current objectives in nanocarbon community. Here, we investigate the local curvature of capped CNTs and define the cap region by a crossover behavior of the curvature energy versus the number of carbon atoms integrated from the tip to the tube region. Clear correlations among the energy gap of the cap localized states, the curvature energy, the number of carbon atoms in the cap region, and the number of specific carbon clusters are observed. The present analysis opens the way to understand the cap states.

Geometry dependence of electronic and energetic properties of one-dimensional peanut-shaped fullerene polymers.

In the present study, we investigate different types of 1D peanut-shaped fullerene polymers (PSFPs) using density functional theory to understand the electronic states and the energetic stability of curved carbon nanomaterials. We generated 53 different models of the 1D PSFPs by means of the generalized Stone-Wales transformations and performed structural optimization for each model. Band structures of the 1D PSFPs exhibit either metallic or semiconducting property according to the geometrical structures. We find that the energetic stability of the 1D PSFPs depends on the geometry: the more octagon and pentagon-octagon pairs (heptagons and hexagon-heptagon pairs) in their geometrical structures, the more stable (unstable) the 1D PSFPs.

Silk gland factor-2, involved in fibroin gene transcription, consists of LIM homeodomain, LIM-interacting, and single-stranded DNA-binding proteins.

SGF-2 binds to promoter elements governing posterior silk gland-specific expression of the fibroin gene in Bombyx mori. We purified SGF-2 and showed that SGF-2 contains at least four gene products: the silkworm orthologues of LIM homeodomain protein Awh, LIM domain-binding protein (Ldb), a sequence-specific single-stranded DNA-binding protein (Lcaf), and the silk protein P25/fibrohexamerin (fhx). Using co-expression of these factors in Sf9 cells, Awh, Ldb, and Lcaf proteins were co-purified as a ternary complex that bound to the enhancer sequence in vitro. Lcaf interacts with Ldb as well as Awh through the conserved regions to mediate transcriptional activation in yeast. Misexpression of Awh in transgenic silkworms induces ectopic expression of the fibroin gene in the middle silk glands, where Ldb and Lcaf are expressed. Taken together, this study demonstrates that SGF-2 is a multisubunit activator complex containing Awh. Moreover, our results suggest that the Ldb·Lcaf protein complex serves as a scaffold to facilitate communication between transcriptional control elements.

Metallic three-coordinated carbon networks with eight-membered rings showing high density of states at the Fermi level.

Using a density functional method to study the electronic structure of various three-coordinated sp(2) carbon nanostructures, we find that the presence of an eight-membered ring adjoined to two five-membered rings in a unit cell brings about the simultaneous occurrence of flat and dispersive bands, quite similar to the band structure of precious metals. These bands are parts of an anisotropic Dirac cone tilted from an isotropic one. We reveal that in-phase and out-of-phase oscillations in the sign of the phase of the Kohn-Sham orbital contribute to the appearance of the unique band structures.

Validity of virial theorem in all-electron mixed basis density functional, Hartree-Fock, and GW calculations.

In this paper, we calculate kinetic and potential energy contributions to the electronic ground-state total energy of several isolated atoms (He, Be, Ne, Mg, Ar, and Ca) by using the local density approximation (LDA) in density functional theory, the Hartree-Fock approximation (HFA), and the self-consistent GW approximation (GWA). To this end, we have implemented self-consistent HFA and GWA routines in our all-electron mixed basis code, TOMBO. We confirm that virial theorem is fairly well satisfied in all of these approximations, although the resulting eigenvalue of the highest occupied molecular orbital level, i.e., the negative of the ionization potential, is in excellent agreement only in the case of the GWA. We find that the wave function of the lowest unoccupied molecular orbital level of noble gas atoms is a resonating virtual bound state, and that of the GWA spreads wider than that of the LDA and thinner than that of the HFA.

Pattern recognition receptors involved in the immune system of hagfish (Eptatretus burgeri).

The initial defense against invading pathogenic microbes is the activation of innate immunity by binding of pattern recognition receptors (PRRs) to pathogen associated molecular patterns (PAMPs). To explain the action of PRRs from hagfish, one of the extant jawless vertebrates, we purified the GlcNAc recognition complex (GRC) from serum using GlcNAc-agarose. The GRC comprises four proteins of varying molecular masses: 19 kDa, 26 kDa, 27 kDa, and 31 kDa. Exposure of Escherichia coli to the GRC led to the phagocytic activation of macrophages, revealing the opsonic function of the GRC. The GRC in serum formed a large complex with a molecular mass of approximately 1200 kDa. The GRC bound to Escherichia coli but not to rabbit red blood cells, despite both having GlcNAc on their surface. These structural and binding properties are similar to those of mannose-binding lectin (MBL). The amino acid sequence of a portion of the 31 kDa protein in the GRC matched the amino acid sequence of variable lymphocyte receptor (VLR)-B in some place. According to the Western blot analysis, the 31 kDa protein was recognized by the anti-hagfish VLR-B antiserum. Based on the results, it appears that the GRC functions as a PRR like MBL and that its 31 kDa protein has a structure similar to that of VLR-B.

Modeling the SDF-1/CXCR4 protein using advanced artificial intelligence and antagonist screening for Japanese anchovy.

SDF-1/CXCR4 chemokine signaling are indispensable for cell migration, especially the Primordial Germ Cell (PGC) migration towards the gonadal ridge during early development. We earlier found that this signaling is largely conserved in the Japanese anchovy (Engraulis japonicus, EJ), and a mere treatment of CXCR4 antagonist, AMD3100, leads to germ cell depletion and thereafter gonad sterilization. However, the effect of AMD3100 was limited. So, in this research, we scouted for CXCR4 antagonist with higher potency by employing advanced artificial intelligence deep learning-based computer simulations. Three potential candidates, AMD3465, WZ811, and LY2510924, were selected and in vivo validation was conducted using Japanese anchovy embryos. We found that seven transmembrane motif of EJ CXCR4a and EJ CXCR4b were extremely similar with human homolog while the CXCR4 chemokine receptor N terminal (PF12109, essential for SDF-1 binding) was missing in EJ CXCR4b. 3D protein analysis and cavity search predicted the cavity in EJ CXCR4a to be five times larger (6,307 Å³) than that in EJ CXCR4b (1,241 Å³). Docking analysis demonstrated lower binding energy of AMD3100 and AMD3465 to EJ CXCR4a (Vina score -9.6) and EJ CXCR4b (Vina score -8.8), respectively. Furthermore, we observed significant PGC mismigration in microinjected AMD3465 treated groups at 10, 100 and 1 × 105 nM concentration in 48 h post fertilized embryos. The other three antagonists showed various degrees of PGC dispersion, but no significant effect compared to their solvent control at tested concentrations was observed. Cumulatively, our results suggests that AMD3645 might be a better candidate for abnormal PGC migration in Japanese anchovy and warrants further investigation.

A GW+Bethe-Salpeter calculation on photoabsorption spectra of (CdSe)3 and (CdSe)6 clusters.

Photoabsorption spectra are calculated for the magic number clusters, (CdSe)(3) and (CdSe)(6), using an all-electron mixed basis GW scheme with the excitonic effect incorporated by solving the Bethe-Salpeter equation (BSE). The GW+BSE calculation provided clear size dependence of the optical gap as expected, while magnitude of the gap is overestimated compared to available experimental one. The gap is found very similarly overestimated when using the local density approximation (LDA) within the density functional theory because accidental error cancellation occurs between the significantly underestimated LDA gap and the excitonic effect neglected therein. The excitonic states are described by superposition of many one-particle states that would not be properly described within a one-particle theory, as clearly visualized in the plot of the exciton wavefunctions.

A relaxin-like peptide purified from radial nerves induces oocyte maturation and ovulation in the starfish, Asterina pectinifera.

Gonad-stimulating substance (GSS) of starfish is the only known invertebrate peptide hormone responsible for final gamete maturation, rendering it functionally analogous to the vertebrate luteinizing hormone (LH). Here, we purified GSS of starfish, Asterina pectinifera, from radial nerves and determined its amino acid sequence. The purified GSS was a heterodimer composed of 2 different peptides, A and B chains, with disulfide cross-linkages. Based on its cysteine motif, starfish GSS was classified as a member of the insulin/insulin-like growth factor (IGF)/relaxin superfamily. The cDNA of GSS encodes a preprohormone sequence with a C peptide between the A and B chains. Phylogenetic analyses revealed that starfish GSS was a relaxin-like peptide. Chemically synthesized GSS induced not only oocyte maturation and ovulation in isolated ovarian fragments, but also unique spawning behavior, followed by release of gametes shortly after the injection. Importantly, the action of the synthetic GSS on oocyte maturation and ovulation was mediated through the production of cAMP by isolated ovarian follicle cells, thereby producing the maturation-inducing hormone of this species, 1-methyladenine. In situ hybridization showed the transcription of GSS to occur in the periphery of radial nerves at the side of tube feet. Together, the structure, sequence, and mode of signal transduction strongly suggest that GSS is closely related to the vertebrate relaxin.

All-proportional solid solution versus two-phase coexistence in the Ti-V alloy by first-principles phase field and SQS methods.

The microstructures of the Ti-V alloy are studied by purely first-principles calculations without relying on any empirical or experimental parameter. The special quasirandom structure model is employed to treat the all-proportional solid solution [Formula: see text] phase, while the first-principles phase field method or its variant is employed to treat the coexistence phases. The linearity of the calculated local free energy against the integer Ti[Formula: see text]V[Formula: see text] composition in the cluster expansion method manifests a clear evidence of the solid solution behavior. From a detailed energy comparison, our results are consistent with the experimental fact that the Ti-V alloy is an all-proportional solid solution of the [Formula: see text] phase at high temperatures and exhibits an [Formula: see text] coexistence at low temperatures. Moreover, it is found that mosaic-type microstructures may appear as a metastable phase, as observed by many experiments. The first-principles criterion for the all-proportional solid solution behavior presented in this paper is very general and can be applied to any other binary or multi-component alloys.