A Novel Intrinsic Interface State Controlled by Atomic Stacking Sequence at Interfaces of SiC/SiO2.

On the basis of ab initio total-energy electronic-structure calculations, we find that electron states localized at the SiC/SiO2 interface emerge in the energy region between 0.3 eV below and 1.2 eV above the bulk conduction-band minimum (CBM) of SiC, being sensitive to the sequence of atomic bilayers in SiC near the interface. These new interface states unrecognized in the past are due to the peculiar characteristics of the CBM states that are distributed along the crystallographic channels. We also find that the electron doping modifies the energetics among the different stacking structures. Implication for performance of electron devices fabricated on different SiC surfaces is discussed.

Interstitial channels that control band gaps and effective masses in tetrahedrally bonded semiconductors.

We find that electron states at the bottom of the conduction bands of covalent semiconductors are distributed mainly in the interstitial channels and that this floating nature leads to the band-gap variation and the anisotropic effective masses in various polytypes of SiC. We find that the channel length, rather than the hexagonality prevailed in the past, is the decisive factor for the band-gap variation in the polytypes. We also find that the floating nature causes two-dimensional electron and hole systems at the interface of different SiC polytypes and even one-dimensional channels near the inclined SiC surface.

Diameter-selective alignment of carbon nanotubes on Si(001) stepped surfaces.

We report total-energy electronic-structure calculations based on the density-functional theory that provide stable adsorption sites, structural characteristics, and energy bands of carbon nanotubes (CNTs) adsorbed on the Si(001) stepped surfaces. We choose (5,5), (9,9), and (13,13) armchair CNTs with the diameters of 6.8 Å, 12.2 Å, and 17.6 Å, respectively, as representatives of CNTs and explore all the possible adsorption sites either on the terrace or at step edges. We find that the (9,9) CNT is most favorably adsorbed at the edge of the double-layer step DB along the ⟨110⟩ direction, whereas the (5,5) and (13,13) CNTs favor the terrace site where the CNTs are perpendicular to the Si dimer rows. This finding is indicative of the diameter-selective self-organized alignment of CNTs by exploiting the Si surface steps along the particular direction. We also find that the electronic structure of each CNT is modified upon adsorption depending on the adsorption site and the diameter of the CNTs. In particular, the (9,9) CNT at the most stable step edge site becomes semiconducting and the resultant valence and conduction bands exhibit nearly linear dispersion with the effective mass of 0.085 m0 (m0: bare electron mass), preserving the characteristics of the Dirac electrons. We also find that the flat bands appear near the Fermi level (EF) when the (13,13) CNT is adsorbed at the metastable DB step edge, inferring that spin polarization is possible for the CNT on the Si(001) stepped surface.

Floating electron states in covalent semiconductors.

We report first-principles electronic-structure calculations that clarify the floating nature of electron states in covalent semiconductors. It is found that wave functions of several conduction- and valence-band states, including the conduction-band minima, do not distribute near atomic sites, as was taken for granted, but float in interstitial channels in most semiconductors. The directions and shapes of the interstitial channels depend on the crystal symmetry so that mysterious variation of the energy gaps in SiC polymorphs is naturally explained by considering the floating nature.

Selective alignment of carbon nanotubes on sapphire surfaces: bond formation between nanotubes and substrates.

We present our first-principles total-energy calculations performed for carbon nanotubes (CNTs) on sapphire substrates. We find that the formation of covalent and partly ionic bonds between Al and C atoms on the Al-rich surfaces causes the selective alignment of CNTs, this being the principal reason for the CNT growth along particular crystallographic directions. We also find that the van der Waals interaction which is important on the stoichiometric surfaces produces no directional preference. The characteristic features in the electron states of the CNT on the substrate are clarified.

Significant change in electronic structures of heme upon reduction by strong Coulomb repulsion between Fe d electrons.

We report total-energy electronic-structure calculations based on the density functional theory performed on a low-spin heme. We have found that the high-lying occupied and low-lying unoccupied states having Fe d and/or porphyrin pi orbital character are significantly rearranged upon the reduction of the heme. An analysis of these states shows that the remarkable elevation of the Fe d levels takes place due to the strong Coulombic repulsion between accommodated d electrons. Due to a peculiarity of the heme, this elevation could be controlled by lower-lying empty porphyrin pi states, leading to electron transfer from Fe d orbitals to the porphyrin pi ones in order to reduce the Coulomb-energy cost. This self-limiting mechanism provides a natural explanation not only for the present calculated results, but also for general electron delocalization appearing under various physiological conditions, regardless of the types of the hemes.

Quantum effects in a cylindrical carbon-nanotube capacitor.

We have theoretically investigated the electric polarization and capacitance in a nano-scale coaxial-cylindrical capacitor made of a double-walled carbon nanotube, (6,0)@(36,0), using a first-principles density-functional method with the enforced Fermi-energy difference scheme. We show that the distribution of the accumulated charge in the inner tube is quantum-mechanically spilled outward, while that in the outer tube is penetrating inward. Reflecting these charge spills, the electrostatic capacitance of the system is larger than what would be expected from classical theory. Furthermore, the total capacitance of the system is smaller than the electrostatic capacitance, which is another quantum effect showing large contributions from the DOS of the electrodes to the capacitance. We believe that these two quantum effects in the capacitance are important for the successful design of carbon-nanotube devices.

First-principles molecular dynamics study of proton transfer mechanism in bovine cytochrome c oxidase.

Density functional based first-principles molecular dynamics calculations, performed on a model system extracted from the bovine cytochrome c oxidase, have been performed in an attempt to inspect the proton transfer mechanism across a peptide group. Our model system includes the specific Tyr440-Ser441 peptide group involved in a novel proton transfer path and shows that the Y440-S441 enol peptide group [-C(OH) = N-], which is a structural isomer of a keto form [-CO-NH-], is the product of the deprotonation of an imidic acid [-C(OH)-NH-] occurring in the vicinity of the deprotonated aspartic acid residue. For the subsequent enol-to-keto tautomerization, a direct H(+) transfer path in the Y440-S441 peptide group has been identified, in which the transition state takes a distorted four-membered ring structure.

Enol-to-keto tautomerism of peptide groups.

Density functional based simulations, performed on polyglycine containing an enol peptide group [-C(OH)N-] which is a structural isomer of a keto form [-CONH-], show that in the enol-to-keto tautomeric reaction, the enol peptide group is less stable than the keto form, and that the enol-to-keto tautomerism is characterized by a cis/trans isomerization of the C-N peptide bond. The rate-limiting step in the cis/trans isomerization is a hydrogen migration from O to N atoms in the peptide group with a transition state consisting of a four-membered ring in the cis configuration. An analysis of the cis/trans isomerization pathway shows that the mechanisms for the cis/trans isomerization are essentially different between the enol and keto forms.

Atom-Scale Reaction Pathways and Free-Energy Landscapes in Oxygen Plasma Etching of Graphene.

We report first-principles molecular dynamics calculations combined with rare events sampling techniques that clarify atom-scale mechanisms of oxygen plasma etching of graphene. The obtained reaction pathways and associated free-energy landscapes show that the etching proceeds near vacancies via a two-step mechanism, formation of precursor lactone structures and the subsequent exclusive CO2 desorption. We find that atomic oxygen among the plasma components is most efficient for etching, providing a guidline in tuning the plasma conditions.

Energy compensation mechanism for charge-separated protonation states in aspartate-histidine amino acid residue pairs.

The initial stage of proton propagation in the D-path channel of bovine cytochrome c oxidase, consisting of the approach of an H(+) to the entrance of this specific pathway, is inspected via first-principles calculations. Our model, extracted from the X-ray crystallographic structure, includes the amino acid residue pair aspartate (Asp91) and histidine (His503) as protonatable sites. Our calculations show that an additional proton, corresponding to the H(+) uptake by the enzyme from the inner bulk water, is transferred to either Asp91 or His503, leading to the formation of a neutral or a charge-separated protonation state. The relative stability between the two states amounts to a total energy difference of about 5 kcal/mol; this indicates that both Asp91 and His503 are involved in the proton supply to the D-path, playing the role of proton acceptors. The hydrogen-bond environment around Asp91 and His503 has an important influence on both the energetics and the electronic structure of the system; for instance, it compensates the Coulomb-energy cost in the charge-separated protonation state. An energy partitioning analysis shows that the compensatory effect is mainly due to local electrostatic interactions among the charged Asp91 and His503 side chains and the surrounding polar residues. The energy compensation mechanism we found in this work balances the energetics of Asp-His pairs, hence permitting an efficient and selective regulation of the protonatable amino acid residues, where several protonation states are accessible within energy differences of the order of a few H-bonds.

Possible mechanism of proton transfer through peptide groups in the H-pathway of the bovine cytochrome c oxidase.

The peptide group connecting Tyr440 and Ser441 of the bovine cytochrome c oxidase is involved in a recently proposed proton-transfer path (H-path) where, at variance with other pathways (D- and K-paths), a usual hydrogen-bond network is interrupted, thus making this proton propagation rather unconventional. Our density-functional based molecular dynamics simulations show that, despite this anomaly and provided that a proton can reach a nearby water, a multistep proton-transfer pathway can become a viable pathway for such a reaction: a proton is initially transferred to the carbonyl oxygen of a keto form of the Tyr440-Ser441 peptide group [-CO-NH-], producing an imidic acid [-C(OH)-NH-] as a metastable state; the amide proton of the imidic acid is then transferred, spontaneously to the deprotonated carboxyl group of the Asp51 side chain, leading to the formation of an enol form [-C(OH)=N-] of the Tyr440-Ser441 peptide group. Then a subsequent enol-to-keto tautomerization occurs via a double proton-transfer path realized in the two adjacent Tyr440-Ser441 and Ser441-Asp442 peptide groups. An analysis of this multistep proton-transfer pathway shows that each elementary process occurs through the shortest distance, no permanent conformational changes are induced, thus preserving the X-ray crystal structure, and the reaction path is characterized by a reasonable activation barrier.

Atomic and electronic structures of carbon nanotubes on Si(001) stepped surfaces.

We report first-principles total-energy calculations that provide energetics and electronic structures of adsorbed carbon nanotubes (CNTs) on stepped Si(001) surfaces. We find that adsorption energies strongly depend on the directions of CNTs, and that there are several metastable adsorption sites both on terraces and near step edges. We also find that the electronic structure of adsorbed metallic CNTs becomes semiconducting or remains metallic, depending on the adsorption site. Charge redistribution upon adsorption is prominent mainly at the CNT-surface interface.

Electronic structure of semiconducting nanotubes adsorbed on metal surfaces.

A total-energy electronic-structure calculation is performed to explore energetics and electronic structures of nanotubes adsorbed on metal surfaces. We find that the charge transfer from metal surfaces to the nanotubes takes place depending on both the electronic structures of the adsorbed nanotubes and the work functions of the metal surfaces. In addition, we also find a substantial hybridization between the electron states of metal atoms and those of the nanotubes, which results in the metal-induced inhomogeneous charge distribution in the nanotubes.

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.

Curvature-induced metallization of double-walled semiconducting zigzag carbon nanotubes.

We report total-energy electronic-structure calculations that provide energetics and electronic structures of double-walled carbon nanotubes consisting of semiconducting (n,0) nanotubes. We find that optimum spacing between the walls of the nanotubes is slightly larger than the interlayer spacing of the graphite. We also find that the electronic structures of the double-walled nanotubes with the inner (7,0) nanotube are metallic with multicarrier characters in which electrons and holes exist on inner and outer nanotubes, respectively. Interwall spacing and curvature difference are found to be essential for the electron states around the Fermi level.

Magnetic ordering of dangling bond networks on hydrogen-deposited Si(111) surfaces.

Based on total-energy electronic-structure calculations within the density-functional theory, we find that a high spin state is realized for an ultimate dangling bond unit on an otherwise hydrogen-covered Si(111) surface. We further propose a systematic method of constructing nanometer-scale dangling bond networks that exhibit the ferrimagnetic spin ordering. The interplay between the electron-electron interaction and the surface reconstruction is elucidated.

Mechanisms of diffusion of boron impurities in SiO2.

We report first-principle total-energy calculations that clarify mechanisms of boron diffusion in SiO2. We find that a B atom takes a variety of stable and metastable geometries depending on its charge state. We also find that atomic rearrangements during the diffusion manifest a wealth of bonding feasibility in SiO2 and that the calculated activation energy agrees with the experimental data available. Recombination enhanced diffusion is also proposed.

E' centers in alpha quartz in the absence of oxygen vacancies: a first-principles molecular-dynamics study.

The displacement of an oxygen atom in pure alpha quartz is studied via first-principles molecular dynamics. The simulations show that when an O atom in a Si-O-Si bridge is moved away from its original equilibrium position, a new stable energy minimum can be reached. Depending on the spin state and charge Q of the system, this minimum can give rise to either a threefold oxygen (singlet ground state and Q=+1) or to an unsaturated Si atom carrying a dangling bond (triplet state). In the latter case, the hyperfine parameters associated with the 29Si dangling bond are in rather good agreement with electron paramagnetic resonance/electron nuclear double resonance experiments.