Charge density functional plus UU calculation of lacunar spinel GaM4_4Se8_8 (M = Nb, Mo, Ta, and W)

Charge density functional plus $U$ calculations are carried out to examine the validity of molecular $J_\text{eff}$=1/2 and 3/2 state in lacunar spinel GaM$_4$X$_8$ (M = Nb, Mo, Ta, and W). With LDA (spin-unpolarized local density approximation)$+U$, which has recently been suggested as the more desirable choice than LSDA (local spin density approximation)$+U$, we examine the band structure in comparison with the previous prediction based on the spin-polarized version of functional and with the prototypical $J_\text{eff}$=1/2 material Sr$_2$IrO$_4$. It is found that the previously suggested $J_\text{eff}$=1/2 and 3/2 band characters remain valid still in LDA$+U$ calculations while the use of charge-only density causes some minor differences. Our result provides the further support for the novel molecular $J_\text{eff}$ state in this series of materials, which can hopefully motivate the future exploration toward its verification and the further search for new functionalities

Optical properties of iron-based superconductor LiFeAs single crystal

We have measured the reflectivity spectra of the iron based superconductor LiFeAs (Tc = 17.6 K) in the temperature range from 4 to 300 K. In the superconducting state (T < Tc), the clear opening of the optical absorption gap was observed below 25 cm-1, indicating an isotropic full gap formation. In the normal state (T > Tc), the optical conductivity spectra display a typical metallic behavior with the Drude type spectra at low frequencies, but we found that the introduction of the two Drude components best fits the data, indicating the multiband nature of this superconductor. A theoretical analysis of the low temperature data (T=4K < Tc) also suggests that two superconducting gaps best fit the data and their values were estimated as {\Delta}1 = 1.59 meV and {\Delta}2 = 3.15 meV, respectively. Using the Ferrell-Glover-Tinkham (FGT) sum rule and dielectric function {\epsilon}1({\omega}), the superconducting plasma frequency ({\omega}ps) is consistently estimated to be 6,665 cm-1, implying that about 59 % of the free carriers in the normal state condenses into the SC condensate. To investigate the various interband transition processes (for {\omega} > 200 cm-1), we have also performed the local-density approximation (LDA) band calculation and calculated the optical spectra of the interband transitions. The theoretical results provided a qualitative agreement with the experimental data below 4000 cm-1Comment: 19 pages, 5 figures. This paper has been accepted for publication in New Journal of Physic

Structural basis for recognition of L-lysine, L-ornithine, and L-2,4-diamino butyric acid by lysine cyclodeaminase

L-pipecolic acid is a non-protein amino acid commonly found in plants, animals, and microorganisms. It is a well-known precursor to numerous microbial secondary metabolites and pharmaceuticals, including anticancer agents, immunosuppressants, and several antibiotics. Lysine cyclodeaminase (LCD) catalyzes ??-deamination of L-lysine into L-pipecolic acid using ??-nicotinamide adenine dinucleotide as a cofactor. Expression of a human homolog of LCD, ??-crystallin, is elevated in prostate cancer patients. To understand the structural features and catalytic mechanisms of LCD, we determined the crystal structures of Streptomyces pristinaespiralis LCD (SpLCD) in (i) a binary complex with NAD+, (ii) a ternary complex with NAD+ and L-pipecolic acid, (iii) a ternary complex with NAD+ and L-proline, and (iv) a ternary complex with NAD+ and L-2,4-diamino butyric acid. The overall structure of SpLCD was similar to that of ornithine cyclodeaminase from Pseudomonas putida. In addition, SpLCD recognized L-lysine, L-ornithine, and L-2,4-diamino butyric acid despite differences in the active site, including differences in hydrogen bonding by Asp236, which corresponds with Asp228 from Pseudomonas putida ornithine cyclodeaminase. The substrate binding pocket of SpLCD allowed substrates smaller than lysine to bind, thus enabling binding to ornithine and L-2,4-diamino butyric acid. Our structural and biochemical data facilitate a detailed understanding of substrate and product recognition, thus providing evidence for a reaction mechanism for SpLCD. The proposed mechanism is unusual in that NAD+ is initially converted into NADH and then reverted back into NAD+ at a late stage of the reaction