Tomomi Shimazaki

Modified Uridines with C5-methylene Substituents at the First Position of the tRNA Anticodon Stabilize U·G Wobble Pairing during Decoding

Post-transcriptional modifications at the first (wobble) position of the tRNA anticodon participate in precise decoding of the genetic code. To decode codons that end in a purine (R) (i.e. NNR), tRNAs frequently utilize 5-methyluridine derivatives (xm5U) at the wobble position. However, the functional properties of the C5-substituents of xm5U in codon recognition remain elusive. We previously found that mitochondrial tRNAsLeu(UUR) with pathogenic point mutations isolated from MELAS (mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes) patients lacked the 5-taurinomethyluridine (τm5U) modification and caused a decoding defect. Here, we constructed Escherichia coli tRNAsLeu(UUR) with or without xm5U modifications at the wobble position and measured their decoding activities in an in vitro translation as well as by A-site tRNA binding. In addition, the decoding properties of tRNAArg lacking mnm5U modification in a knock-out strain of the modifying enzyme (ΔmnmE) were examined by pulse labeling using reporter constructs with consecutive AGR codons. Our results demonstrate that the xm5U modification plays a critical role in decoding NNG codons by stabilizing U·G pairing at the wobble position. Crystal structures of an anticodon stem-loop containing τm5U interacting with a UUA or UUG codon at the ribosomal A-site revealed that the τm5U·G base pair does not have classical U·G wobble geometry. These structures provide help to explain how the τm5U modification enables efficient decoding of UUG codons.

Controlling formation of single-molecule junctions by electrochemical reduction of diazonium terminal groups.

We report controlling the formation of single-molecule junctions by means of electrochemically reducing two axialdiazonium terminal groups on a molecule, thereby producing direct Au-C covalent bonds in situ between the molecule and gold electrodes. We report a yield enhancement in molecular junction formation as the electrochemical potential of both junction electrodes approach the reduction potential of the diazonium terminal groups. Step length analysis shows that the molecular junction is significantly more stable, and can be pulled over a longer distance than a comparable junction created with amine anchoring bonds. The stability of the junction is explained by the calculated lower binding energy associated with the direct Au-C bond compared with the Au-N bond.

Energy band structure calculations based on screened Hartree-Fock exchange method: Si, AlP, AlAs, GaP, and GaAs.

The screening effect on the Hartree-Fock (HF) exchange term plays a key role in the investigation of solid-state materials by first-principles electronic structure calculations. We recently proposed a novel screened HF exchange potential, in which the inverse of the dielectric constant represents the fraction of the HF exchange term incorporated into the potential. We demonstrated that this approach can be used to reproduce the energy band structure of diamond well [T. Shimazaki and Y. Asai, J. Chem. Phys. 130, 164702 (2009)]. In the present paper, we report that the screened HF exchange method is applicable to other semiconductors such as silicon, AlP, AlAs, GaP, and GaAs.

First principles band structure calculations based on self-consistent screened Hartree–Fock exchange potential

A screened Hartree-Fock (HF) exchange potential with the dielectric constant was previously reported by Shimazaki and Asai [Chem. Phys. Lett. 466, 91 (2008)], in which the inverse of the dielectric constant was used to represent a fraction of the HF exchange term. In that report, the experimentally obtained value for the dielectric constant was employed. Herein, we discuss a self-consistent technique, in which the value of the dielectric constant can be automatically determined. This technique enables the energy band structure to be determined without using the experimental value. The band energy structure of diamond is calculated, a self-consistent procedure is determined to give closer bandgaps compared with the local density approximation and the generalized gradient approximation.

Fate of methanol molecule sandwiched between hydrogen-terminated diamond-like carbon films by tribochemical reactions: tight-binding quantum chemical molecular dynamics study

Recently, much attention has been given to diamond-like carbon (DLC) as a solid-state lubricant, because it exhibits high resistance to wear, low friction and low abrasion. Experimentally it is reported that gas environments are very important for improving the tribological characteristics of DLC films. Recently one of the authors in the present paper, J.-M. Martin, experimentally observed that the low friction of DLC films is realized under alcohol environments. In the present paper, we aim to clarify the low-friction mechanism of the DLC films under methanol environments by using our tight-binding quantum chemical molecular dynamics method. We constructed the simulation model in which one methanol molecule is sandwiched between two hydrogen-terminated DLC films. Then, we performed sliding simulations of the DLC films. We observed the chemical reaction of the methanol molecule under sliding conditions. The methanol molecule decomposed and then OH-termination of the DLC was realized and the CH3 species was incorporated into the DLC film. We already reported that the OH-terminated DLC film is very effective to achieve good low-friction properties under high pressure conditions, compared to H-terminated DLC films. Here, we suggest that methanol environments are very effective to realize the OH-termination of DLC films which leads to the good low-friction properties.

Electronic Structure Calculations under Periodic Boundary Conditions Based on the Gaussian and Fourier Transform (GFT) Method.

We developed the Gaussian and Fourier transform method for crystalline systems. In this method, the Hartree (Coulomb) term of valence electron contribution is taken into account by solving the Poisson equation based on Fourier transform technique. We compared the band structures obtained by the Hartee-Fock (HF) approximation and the density functional theory (DFT). We used three different types of density functional approximations such as the local density approximation (LDA), generalized gradient approximation (GGA), and hybrid density functional. In this paper, we confirm that our calculation technique yields similar results to previous studies.

A theoretical study of molecular conduction. II. A Hartree-Fock approach to transmission probability

In this paper, we discuss molecular conductivity based on Greens function methods. In our calculations, we adopted the self-energy formalism to accommodate semi-infinite electrodes connected to a molecule, and the self-energy was obtained from the surface Greens function of the electrodes. We adopted the formalism of the surface Greens function derived by Sanvito et al. [Phys. Rev. B 59, 11936 (1999)] and Krstic et al. [Phys. Rev. B 66, 205319 (2002)], and although their formalisms for the surface Greens function were different, we were able to demonstrate that these formalisms are mathematically identical. We analyzed the electron transmission probability by using the spectrum expression of Greens function, instead of using the inverse matrix of the effective Hamiltonian that includes an isolated molecule and the electrodes. Finally, we calculated the transmission probability of benzenedithiol based on the Hartree-Fock method and analyzed the disappearance of the transmission probability due to the orbital interference.

Theoretical study of a screened Hartree–Fock exchange potential using position-dependent atomic dielectric constants

Dielectric-dependent screened Hartree-Fock (HF) exchange potential and Slater-formula have been reported, where the ratio of the HF exchange term mixed into potentials is inversely proportional to the dielectric constant of the target semiconductor. This study introduces a position-dependent dielectric constant method in which the dielectric constant is partitioned between the atoms in a semiconductor. These partitioned values differ depending on the electrostatic environment surrounding the atoms and lead to position-dependent atomic dielectric constants. These atomic dielectric constants provide atomic orbital-based matrix elements for the screened exchange potentials. Energy band structures of several semiconductors and insulators are also presented to validate this approach.

Dielectric-dependent screened Hartree–Fock exchange potential and Slater-formula with Coulomb-hole interaction for energy band structure calculations

We previously reported a screened Hartree-Fock (HF) exchange potential for energy band structure calculations [T. Shimazaki and Y. Asai, J. Chem. Phys. 130, 164702 (2009); T. Shimazaki and Y. Asai, J. Chem. Phys. 132, 224105 (2010)]. In this paper, we discuss the Coulomb-hole (COH) interaction and screened Slater-formula and determine the energy band diagrams of several semiconductors, such as diamond, silicon, AlAs, AlP, GaAs, GaP, and InP, based on the screened HF exchange potential and Slater-formula with COH interaction, to demonstrate the adequacy of those theoretical concepts. The screened HF exchange potential and Slater-formula are derived from a simplified dielectric function and, therefore, include the dielectric constant in their expressions. We also present a self-consistent calculation technique to automatically determine the dielectric constant, which is incorporated into each self-consistent field step.

Communication: The reason why +c ZnO surface is less stable than −c ZnO surface: First-principles calculation

It has been experimentally shown that an O(-c)-polar ZnO surface is more stable than a Zn(+c)-polar surface in H(2) ambient. We applied first-principles calculations to investigating the polarity dependence on the stability at the electronic level. The calculations revealed that the -c surface terminated with H atom was stable maintaining a wurtzite structure, whereas the +c surface was unstable due to the change of coordination numbers of Zn at the topmost surface from four (wurtzite) to six (rock salt). This causes the generation of O(2) molecules, resulting in instability at the +c surface.