Energy exchange network of inter‐residue interactions within a thermally fluctuating protein molecule: A computational study

Protein function is regulated not only by the structure but also by physical dynamics and thermal fluctuations. We have developed the computer program, CURrent calculation for proteins (CURP), for the flow analysis of physical quantities within thermally fluctuating protein media. The CURP program was used to calculate the energy flow within the third PDZ domain of the neuronal protein PSD‐95, and the results were used to illustrate the energy exchange network of inter‐residue interactions based on atomistic molecular dynamics simulations. The removal of the α3 helix is known to decrease ligand affinity by 21‐fold without changing the overall protein structure; nevertheless, we demonstrated that the helix constitutes an essential part of the network graph. © 2015 Wiley Periodicals, Inc.     

Structure,energy and solute segregation behaviour of [110] symmetric tilt grain boundaries in yttria-stabilized cubic zirconia

Yttria-stabilized cubic zirconia bicrystals with [110] symmetric tilt grain boundaries are systematically fabricated by the diffusion bonding method. It is revealed that the grain-boundary atomistic structures, excess energies and solute segregation behaviours are strongly dependent on the macroscopic geometries of the boundaries. High-resolution transmission electron microscopy combined with lattice statics calculations suggests that the grain-boundary structures are characterized by the accumulation of coordination-deficient cation sites at their cores, whose densities have a clear correlation with excess energies and amounts of solute segregation. The orientation dependence of grain-boundary properties in cubic zirconia can thus be linked and understood via local grain-boundary atomistic structures with the characteristic miscoordinated cation sites.     

Unified approach to catechin hetero-oligomers: first total synthesis of trimer EZ-EG-CA isolated from Ziziphus jujuba

A catechin hetero-trimer isolated from Ziziphus jujuba has been synthesized. Among three constituent monomers, (-)-epiafzelechin and (-)-epigallocatechin were prepared by de novo synthesis. Trimer formation relied on the unified approach to oligomers based on the bromo-capping and the orthogonal activation, reaching the reported structure of the natural product.     

First-principles supercell calculations for simulating a shallow donor state in Si

We present first-principles simulations of As-doped Si carried out using several cubic supercells of up to 10 648 atoms. The 1s As donor level in each supercell splits into three states, which have A₁, T₂, and E symmetries, respectively. The 1s(A₁) wavefunction is well converged in the largest cell, and its spread is close to those of the effective-mass theories. However, the calculated binding energies are smaller than experimental values. This discrepancy would be due to the self-interaction error within the approximated exchange-correlation density functional used in this calculation. Therefore, we also show perturbative calculations based on an impurity potential without the self-interaction error to estimate the binding energies of the 1s(A₁) donor state. The estimated binding energy in the largest supercell agrees well with the experimental value.     

Bis‐copper(II) Complex of Triply‐linked Corrole Dimer and Its Dication

Copper complexes of corroles have recently been a subject of keen interest due to their ligand non‐innocent character and unique redox properties. Here we investigated bis‐copper complex of a triply‐linked corrole dimer that serves as a pair of divalent metal ligands but can be reduced to a pair of trivalent metal ligands. Reaction of triply‐linked corrole dimer 2 with Cu(acac)₂ (acac=acetylacetonate) gave bis‐copper(II) complex 2Cu as a highly planar molecule with a mean‐plane deviation value of 0.020 Å, where the two copper ions were revealed to be divalent by ESR, SQUID, and XPS methods. Oxidation of 2Cu with two equivalents of AgBF₄ gave complex 3Cu , which was characterized as a bis‐copper(II) complex of a dicationic triply‐linked corrole dimer not as the corresponding bis‐copper(III) complex. In accord with this assignment, the structural parameters around the copper ions were revealed to be quite similar for 2Cu and 3Cu . Importantly, the magnetic spin–spin interaction differs depending on the redox‐state of the ligand, being weak ferromagnetic in 2Cu and antiferromagnetic in 3Cu .     

Isospin properties of () reactions for the formation of deeply-bound antikaonic nuclei

The formation of deeply-bound antikaonic nuclear states in nuclear (K⁻,N) reactions is investigated theoretically within a distorted-wave impulse approximation (DWIA), considering the isospin properties of the Fermi-averaged elementary amplitudes. We calculate the formation cross sections of the deeply-bound states by the (K⁻,N) reactions on the nuclear targets, ¹²C and ²⁸Si, at incident K⁻ lab momentum p_K⁻=1.0 GeV/c and θ_lab=0°, introducing a complex effective nucleon number N_eff for unstable bound states in the DWIA. The results show that the deeply-bound states can be populated dominantly by the (K⁻,n) reaction via the total isoscalar ΔT=0 transition owing to the isospin nature of the amplitudes, and that the cross sections described by ReN_eff and ArgN_eff enable to deduce the structure of the nuclear states; the calculated inclusive nucleon spectra for a deep -nucleus potential do not show distinct peak structure in the bound region. The few-body and states formed in (K⁻,N) reactions on s-shell nuclear targets, ³He, ³H and ⁴He, are also discussed.     

The effect of thickness and annealing condition on the microstructure and magnetic properties of Fe/Pt multilayer thin films

[Fe(0.5 nm)/Pt(0.5 nm)]₄₀, [Fe(1 nm)/Pt(1.5 nm)]₂₀ and [Fe(3 nm)/Pt(3 nm)]₁₀ multilayer were prepared by DC magnetron sputtering. By conventional furnace annealing (CA) at 270–600 °C for various time, all of the films still remained the disordered structure with the soft magnetic phase. By rapid thermal annealing (RTA) at 500 °C for various time, we obtained the [Fe(1 nm)/Pt(1.5 nm)]₂₀ and [Fe(3 nm)/Pt(3 nm)]₁₀ films with L1₂ ordered FePt₃ phase which was almost ferromagnetic at room temperature. However, the [Fe(0.5 nm)/Pt(0.5 nm)]₄₀ films was still disordered state even under RTA. Compared with CA, RTA exposed an outstanding effect on accelerating the phase transition when the film thickness is over [Fe(0.5 nm)/Pt(0.5 nm)]₄₀.